I just did one of these, literally yesterday. It's true you'll get that error message and it will ask if you want to correct the size error. If you do, it will make the database stop working. I just erased everthing on the card though, and the HMI re-created the database just fine. Also, if you have trouble getting the logging to work, remember that the CF-card slot is seen by the HMI as "StorageCard2".
Cheers!