I had a NON O multiple entries. After like 80 days I have spent some days in Penang. Then returned back to BKK and stayed there for another 4 weeks about. In total about like 125 days
I faced the same problem early this year. I got a new passport from German embassy. I went to Chaeng Wattana to transfer my NON O and they send me home saying no problem. I went out to Malaysia and returned back to Thailand a few days later without any issue. Got anther 90 days.