Issue Summary

Searching for some project scoped fields with IS EMPTY operator gives inaccurate results. 

Steps to Reproduce

1. Have at least two custom fields with the same name (e.g. Component) and scope to different projects or between global and project scope (e.g. custom field 10000 scoped to project A and custom field 10001 scoped to project B)
2. Try to find issues from project A that don't have Component field set

project = A AND Component IS EMPTY

OR
The issue is also experienced when only one custom field is present but a context is applied to limit the custom field to certain projects.

Expected Results

Search checks value only of Component field scoped to given issue (project).

In our example search should return issues from project A that don't have value in Component field that is scoped to project A (custom field 10000). Issues from project A that don't have value in Component field 10001 should be ignored as that custom field is scoped to project B.

Actual Results

Search checks checks all Component fields (ignores that some of them are not in project scope).

In our example search currently returns all issues from project A as they don't have value in Component field that is scoped to project B (10001).

Workaround

Refer in your JQL search to the custom field by id, ie:

project = A AND cf[10000] IS EMPTY

instead of

project = A AND Component IS EMPTY

To find id of custom field scoped to given project use GET /rest/api/3/field resource.