I have a user who deleted a duplicate project (it had the same name but a different project key). Now the project still shows up in the list of projects on the dashboard but when the user clicks on the project name it displays a 500 error page.
I tried reindexing to see if that would fix it and of course it didn't. (that would be too easy).
Oof, I've seen that, but only when the deletion was interrupted. I was able to fix it by re-indexing (as you've already tried), then running the integrity checker, then trying to delete the project again.
The second delete attempt seemed to work, but I seem to remember that it needs a bit of thought to get to it - you need to work out the url and project ID and hit it directly, as trying to get there from the main screens falls over. (i.e, for v4, https://yourjiraserver/secure/admin/DeleteProject!default.jspa?pid=11380 )
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