A custom field with a project or issue type context may not appear on the search bar in basic mode. Three ways to bring it back.
You can:
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Remove the Issue Type context from the custom field to re-enable the field in Basic mode
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Change the Issue Type context to project based context
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Add the custom field as default search field
Detailed explanation of the issue, including workarounds: https://confluence.atlassian.com/jirakb/custom-field-not-appearing-in-issue-navigator-search-criteria-125698089.html