@techbill, problems apparently start when you (try to) convert the database from MYISAM to InnoDB or/and change collation - utf8_unicode_ci or utf8mb4_sumthing_?
I think I’ve solved my original issue related to that, but my database is now a mix of InnoDB and MYISAM - some MYISAM tables won’t convert, not sure if I’d only cause more problems if I forced it somehow. Also not sure what recommended collation etc. is.
I am still curious to see an answer to the original question of this thread, how to do a clean surgical rebuild of the database without losing data and without having to reinstall everything.