I deleted a folder from /var/lib/mysql and now all of my databases seem to be unaccessible
mysqlcheck won't help, it's for damaged files.
You should have deleted non-table files in the directory, not the directory itself. Especially if you use MySQL 8, as I suspect. Because your tables metadata are stored in an internal dictionary.
Anyway, don't you have a backup?
If not, recreate the directory and try running individual DROP TABLEs. It may work or not. Let me know how it goes.