Problem Definition:

The KB Advanced searching - operators reference For the *DOES NOT CONTAIN: Unable to render embedded object: File (~* operator variable there needs to be clarification on the results of EMPTY values, all the other NOT reference examples () not found.= , NOT IN, IS NOT, WAS NOT, WAS NOT IN) include this information to include the EMPTY set just not for the !~ section

For the The Example:

Note that for version fields, the ~ operator returns an exact match. For example, to find issues where Fix Version is not "9.0", you would use the following query:

fixVersion !~ "9.0"

This JQL Would be any issue that has a value in the fix version field that is not 9.0 but would not include issue where the FixVersion field was empty to do this the Filter would need to include:

fixVersion !~ "9.0" OR fixVersion is empty

The main take away is that when you are using a Exclude statement in JQL the Logic is such that a value is expected in the Field that does not match the value given, so you must include an additional search for the Empty set as NULL is not a value