I got the same situation with you. The only way is to do the 90D report at MTT and pay 2K, otherwise they reserve the right to reject your next extension in Nov.
Immigration officer need your fingerprints before passing through Thai border. No matter how many passports you have, your in/out record has shown on the system clearly. I switch 2 passports in and out Thailand many time before but it's doesn't work right now.