Then you'd need to apply for a reentry permit before you leave so you can re-enter with you Non-O.
Also, you need to apply for a 1 year extension of your Non-O. The time varies by office but I believe Bangkok is 15 days before expiration, I'll have to confirm that though.
If you don't complete your 1 year extension before you leave the country, and your 90 day Non-O expires while you're outside of Thailand, you'll have to restart the process (either by applying for a new Non-O in the USA or entering Thailand visa exempt and applying for a new Non-O in country).