That is likely the cause of your problems.
Tables should not be deleted, they should be DROP-ped.
IMHO mucking about in the database folders is not the best idea.
Have you tried a CHECK TABLE query?
https://dev.mysql.com/doc/refman/5.0/en/check-table.html
or a REPAIR TABLE query?
https://dev.mysql.com/doc/refman/5.1/en/repair-table.html