This sounds like a bug; if so I'll file it anyway, but perhaps this sounds familiar to some.
I have a saved filter. One criterium is the selection of a certain value (custom field, multiple values possible to be selected simultaneously). Now I added some more possible values and slightly renamed the to-be selected value.
The search results yielded about 60 issues first, now only about 30. When looking at the missing ones, nothing seems to be wrong, they do match the search criteria including the custom field value.
After a warning in the Issue Navigator (in advanced searching) that the value could not be found anymore, I changed it in the filter to the new value and saved. Strangely, in Simple Searching or using the filter shortcut itself, no warnings are seen. A similar filter that I have is still unchanged, also delivers about 50% of the expected results and states the 'old' value in the summary of the filter, still yielding the (about 50%) of issues with the renamed value...
When I manually edit a missing issue and simply re-enter the to-be selected value of the custom field, the issue reappears in the search results after refreshing in the Issue Navigator. However, this means that any other values that were selected need to be deleted first and added back later (or any other should be added first and deleted later; i.e. 'something' needs to be changed in the selected values).
Also completely new searches reveal the problem, even when only selecting the Project and that one to-be selected value.
It sound as the JIRA indexes got messed up after you renamed the fields, and it appears you've not re-index after doing so. If making any changes in any of the following areas, it is advised to re-index JIRA to avoid these kind of problems:
I hope this helps!
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