Oh wait, I thought you meant the actual table indexes on the database level were not transfered to the new database.
If it took you 12 hours, that could mean that the counting process simply fails and reports back 0. In MySQL/MariaDB databases counting large number of rows can timeout very easily – it is a known flaw. You probably have multi million rows and that explains it.
Your data is very likely completely fine if you migrated, the counter is only reporting the incorrect numbers.