I was in the same situation last year. I had an ED visa from a language school and I left Thailand for a week, maybe a little more. I didn't have a specific reason, I just wanted to go to my home country and see my family. I was afraid to come back given all the comments and scary stories I had read in this group. I had 20,000 baht in cash with me and all kinds of documents I could get from my school.
Do you know what happened? Nothing. They didn’t ask me a single question and just let me in.
I'm afraid the extensions are only for 1 or 2 months now. I got an ED visa this year in Bangkok which was for 90 days as you say, but all the extensions are either 30 or 60 days long.
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