Cobb won't be able to do anything about it, the protection is within the ECU itself, so regardless of vendor they (VW) will be able to detect ECU reprogramming.
When you marry the cobb for the first time, it takes a snap shot of the ECU (this is why initial marrying takes 20-25 minutes). Once you unmarry the COBB AP it places the pre-tune data/snapshot/image whatever you want to call it back into place and it doesn't not trigger the flash counter.
**Based on my understanding**