We have fall into a big trouble on our cpanel server. The issue is that some tables of some dbs are most likely corrupted. It neither allows us to drop it nor restores from backup completely. Most of sites are having database issue.
For drop, it says "can't rmdir errno 39
For restore, no error but restoring backup doesn't help much.
The database directory contains some non-MySQL files. Look in the filesystem for this particular db - maybe something in that directory will give you a hint as to why it fails. Or you can move them to a different directory and retry the drop.