Summary Note:

While the summary was how the issue described herein was discovered, the Kanban board and filters are not the root cause. I use this summary because it may be more helpful to others who discover the same issue.

Relevant Links

Relates to Why is a JIRA issue with an EMPTY fixversion retured in query results? and I have a comment on the OP.
Workflow assigns user but email notification doesn't say assignee changed support ticket where I was told to raise this issue myself.

Steps to Discover Existing Root Cause Issue

Any hits on the following query: fixVersion NOT in releasedVersions() AND fixVersion NOT in unreleasedVersions() and fixVersion is not EMPTY. A hit on this query is the basis for this issue.

Steps to Reproduce

Atlassian JIRA Project Management Software (v6.4.3#64018-sha1:4550402)
One set of steps to reproduce (note that once the problem is produced, there is not a known way to undo it so preferably do not perform this on something you want to appear on a Kanban board otherwise append OR fixVersion NOT in releasedVersions() to the default subfilter):

1. Create a test issue or navigate to an existing issue
2. Fill in the fix Version/s field with an existing version (a new version created from field entry was not tested)
3. Navigate to the project management page and manage the versions
4. Choose to delete the version that you associated with the aforementioned issue, as shown in attachment.
5. When prompted that "there are issues related to this version, specify what is to be done with them" select "remove version" (the other option of swap was not tested)
6. Run the following query with or without the ID for that issue and the issue will appear in the search results fixVersion NOT in releasedVersions() AND fixVersion NOT in unreleasedVersions() and fixVersion is not EMPTY AND ID = DMZ-48 (where DMZ-48 is the ID of the issue being worked) or fixVersion NOT in releasedVersions() AND fixVersion NOT in unreleasedVersions() and fixVersion is not EMPTY and also the issue will drop of a Kanban board if it was there before and the board uses the default sub filter.

There may be other steps to reproduce, and they may not be isolated to the release manager. Let me know if anyone finds other steps that reproduce the issue.

Workaround:

The workaround for after this issue has already occurred is to include a fix version that is unreleased OR to change the subfilter to say fixVersion in unreleasedVersions() OR fixVersion is EMPTY OR fixVersion NOT in releasedVersions() should be ok short term. The filter change workaround may induce performance issues in the long term.

Preventative Action:

Proven proper way is to delete a version from the issues it is contained in BEFORE deleting it from the version manager:

1. Run the JQL query on the version you want to remove fixVersion = "Test 1" and may also need to be done for affected version.
2. Perform a bulk operation on all issues to "Change Fix Version/s" select field action "Find and remove these" and type in the version to delete.
3. JQL query on the issue ID itself fixVersion NOT in releasedVersions() AND fixVersion NOT in unreleasedVersions() and fixVersion is not EMPTY AND ID = DMZ-48 or without the ID fixVersion NOT in releasedVersions() AND fixVersion NOT in unreleasedVersions() and fixVersion is not EMPTY should not return the issue that this operation was performed on and also the issue will stay on a Kanban board if it was there before and the board uses the default sub filter.

Speculation:

If there is a special flag parameter for "fixVersion is not EMPTY" then it may not have been changed properly. May have something to do with NULL rather than EMPTY. fixVersion NOT in releasedVersions() AND fixVersion NOT in unreleasedVersions() and fixVersion is not EMPTY. It should be obvious that this query should not return any results. If it is not in the released version list or the unreleased version list, then the fix version field should be empty because in theory the fix version is either released or unreleased. Since the release manager maintains the version list, but the fixVersion field itself is independent of the release manager lists, then there has been some kind of decoupling that has occurred.

Additional Work and Speculation

The below text includes queries for a specific project, but the problem was not isolated to that project as is discovered about half way through.

Added a fix version to an issue that never had one before, then I removed it and it did not have the issue discussed below. So simply deleting the fix version field does not break it.

I thought a possible root cause is that the issue was moved to a different project, thus stripping the version fields since the versions are specific to a project. I think the long term preventative workaround is to clear the affected and fix version fields before moving the issue to another project.

Since the history shows that the workflow has been changed, it is possible that the workflow was changed due to a move. I know that I probably moved issues between projects to manually reset the state they were in rather than running it through the entire workflow or in some cases there were states that only occurred initially.

The tracking down the root cause work is described below;

The subfilter is the one filtering it out, but that is not the root cause. The primary filter project = FFAA ORDER BY Rank ASC only searches for items in that specific project and then sorts them. The subfilter (and this is set by default and can be changed) is fixVersion in unreleasedVersions() OR fixVersion is EMPTY and the description states

"Further filtering of issues for unreleased work."

The root cause is revealed with the result of this query:
project = FFAA AND NOT fixVersion in releasedVersions() AND NOT fixVersion in unreleasedVersions()
Apparently the JIRA record still includes the fix version that shows up in the history, but it neither appears in "releasedVersion()" nor "unreleasedVersion()" since the release manager does not contain that version.

Added "EP-SYS-9526 Rev A" to the release manger but the unique ID "[ 10002 ]" will likely not be the same. When adding the fix version under question, that did not fix the issue. And when deleting the temporary fix version under question I was given this notice

There are no issues related to this version. It is safe to delete.

Ran this query project = FFAA AND NOT fixVersion in releasedVersions() AND NOT fixVersion in unreleasedVersions() and performed a bulk operation on all 15 issues to "Change Fix Version/s" to "Clear field" but that did not fix it because the query still shows those versions so the field is infact cleared...

project = FFAA AND NOT fixVersion in releasedVersions() AND NOT fixVersion in unreleasedVersions() AND fixVersion is EMPTY yields no results but project = FFAA AND NOT fixVersion in releasedVersions() AND NOT fixVersion in unreleasedVersions() AND fixVersion is not EMPTY yields the that should be showing up on the Kanban board related issues.

project = FFAA AND fixVersion is not EMPTY yields includes issues that should be showing up on the Kanban board along with others from other projects, but those issues are all included even though when showing the column for the fix version it appears to be empty. project = FFAA AND fixVersion = "EP-SYS-9526 Rev A" yields not results so there may be a flag set somewhere that didn't get cleared when the field was cleared, and since the clearing didn't appear in the history it would seem that the field wasn't cleared properly.

with a bulk operation to replace what was existing in those issues with a fix and affected version. :

Kalen Brown made changes - 2 minutes ago
Affects Version/s EP-SYS-9526 Rev OR [ 10419 ]
Affects Version/s EP-SYS-9526 Rev OR [ 10419 ]
Fix Version/s EP-SYS-9526 Rev A [ 10418 ]
Fix Version/s EP-SYS-9526 Rev A [ 10418 ]

Unsure why it shows up twice. After performing this operation and including a fix version that hasn't been released, it now shows up on the Kanban board. But since the issues that I just performed the bulk edit on are not planned to be fixed in a release (which is why the version was deleted in the first place), the fix version will be cleared again to see if the same queries still show a hidden problem. Bulk operation to Change Fix Version/s operation of Clear field. This did NOT fix the problem as now it does not show up on the Kahban board and the issues that should be showing up on the Kanban board appear with the query project = FFAA AND fixVersion is not EMPTY even though the column shows it is cleared. An XML and Excel of the query fixVersion != EMPTY shows that there are 22. In the excel export, the "fixVersion" field is infact empty and contains no characters including white space. In the XML export, it shows the query I performed and shows fix versions on some but not on others. The field is not even shown in the XML export for the issues that do not have anything in their fix version field. So, as far as I can tell, functionally the field is empty.

One of the 22 was edited individually to see if a bulk operation was not fixing it. When the fix version was added, then it was removed from the result of the following query, but once the fix version was deleted then it was a listed result in the following query. In the log it says the Fix Version/s was changed from the original value of "Test 1 [ 10400 ]" and then has nothing, not even a unique identifier, in the new value column. It seems that DMZ-26 suffers the same history problem where the Fix Version/s of "1 [ 10100 ]" was entered but was never shown as removed. The history shows that the workflow was changed and that was the "only" change shown in the history.

I have attempted the integrity check, re-index, filling in the field and then clearing it both with an individual and bulk operation, and I can't make it so that JIRA thinks the fix version field is cleared. The related link has an answer that suggests a SQL query, but I will have to request specific permission to mess with the SQL database directly. I am the JIRA administrator for our instance, but I am not the administrator of the server itself.

if fixVersion NOT in releasedVersions() AND fixVersion NOT in unreleasedVersions() and fixVersion is not EMPTY then where and what is it? It must think there is a fix version but I can't see what it is.