First of all you did not state that the search is partially working. You just stated that the search doesn't work that would imply its totally broken. Lets keep a polite tone.
What version of JIRA are you on?
This reminds me of the filter search bug for boards. https://jira.atlassian.com/browse/JSW-11403
I have multiple projects that use variations of the same base workflow. The variations depend on the requirements of the project or issue type. The variations mostly come in the form of new statuses ...
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