Next time we can try https://www.whonix.org/wiki/Main_Page?action=purge (requires wiki admin). But I doubt it will help since a null edit (edit, save without actual changes) should do the same, but didn't.
A while ago before we had this powerful server, whonix.org was slow. So I went crazy on caching. Nowadays it causes issues. I don't know if its wise to disable the file cache. Having mediawiki php process the page on every anonymous page visit may be too much.
I am reading https://www.mediawiki.org/wiki/Manual:File_cache#Expiration but not getting any wiser.
Perhaps the unclean but easiest resolution would be to automate pruning
/var/www/w/cache/* and varnish purge every day or every hour or so.