Just to double check:
I am on a 1 year extension of stay and shortly before my 90 day report is due, I will leave the country and be back by reentry permit a couple of weeks later. That means my 90 days will begin to count again from the day I return to Thailand, right? Hence I can ignore the original due date, correct?
TLDR : Answer Summary
If you leave Thailand shortly before your 90-day reporting is due and return with a reentry permit, your 90-day countdown will restart from the date of your reentry into Thailand. You can disregard the original 90-day report due date.