I never tried to restore backups from different country code controllers. I don't even know if restoring a flash backup will change the country code of a controller as that code is not expected to change after the initial installation. The only way I know is by doing a full 'write erase all' and start all over.
If you have Airwave, you can fetch the old controller config in Airwave, then push it back to your new controller that you configured to the correct country code. You will lose stuff like your AP database, but if you enable automatic whitelisting, that database should be recreated pretty quickly (AP's will go through a few reboots, so the process may take may be 15 minutes before your AP's return.
Also, for a Rest-of-World controller, which you have as both FR and CZ are outside the US, you can set different country codes on you AP Groups through the AP regulatory domain profile. That AP Group regulatory domain profile may be different from the controller regulatory domain. So having the controller domain to another country is not a real problem, however I would personally like to have that set to a logical country as others looking at your controller may be confused by a 'wrong' regulatory domain.
Summarized:
Option 1: Leave it as is; and use the AP regulatory domain in the AP groups to get the right setting.
Option 2: Try is a flash restore leaves the country and use the flash backup/restore procedure to fix.
Option 3: Migrate the config with Airwave, or manual in a text file, which will clear your ap database, local user database, installed certificates that you may need to reinstall if used.
Herman