Hi, next time please post in either New Beta C.O.R.E. 0.7 or C.O.R.E. Bugs.
To answer your question, they have been disbanded. What happened after the destruction of Czechoslovakia and the creation of Slovakia is that virtually EVERY Czechoslovakian unit became part of the Slovakian army. This causes multiple problems.
#1. How can Germany reasonably get captured Czech tanks when Slovakia is using all of the former Czech tanks?
#2. The bulk of the Czechoslovakian army was made up of Czech citizens, who were not keen, or possibly even allowed, to be armed and in the Slovakian armed forces.
So, the destruction of the Czech army is historic, and improves gameplay, as Slovakia won't start with an overly powerful military, capable of destroying Poland on their own.