Users can still access spaces if they have the link but we need the index back up for general access - any hints on how to do this?
One of the reasons this can happen is a recent Confluence upgrade. Or it can be a problem with indexing. Or can be some unknown factor.
In any case, please try rebuilding the index by navigating to Confluence Admin > Content Indexing > Rebuild.
There is also a KB article from Atlassian that might help you - https://confluence.atlassian.com/confkb/spaces-are-missing-from-the-space-directory-296093273.html, talks about how to solve such issues.
Hope one of the methods works for you!
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