There are three separate DXCC entities involving OK, OL & OM callsigns, as follows:

Czechoslovakia 218 Deleted
Czech Republic 503 Current
Slovak Republic 504 Current

The above information is taken from the ADIF specification,

How is all this related to dates and prefixes?

DXCC Valid QSO Dates Prefixes
Czechoslovakia Before 1993-01-01 OK OL OM
Czech Republic 1993-01-01 to now OK OL (ex OK1, OK2)
Slovak Republic 1993-01-01 to now OM (ex OK3)

The above information is from the RSGB Prefix Guide.

Why do I get error messages about OK, OL & OM in my upload report?

You get these messages in cases where your logging software does not map these callsigns according to the above information.
In these cases, you should encourage the person who maintains your logging software's country database to update the mappings in accordance with the above.