is this something specific for extensions based on work? My experience is that a marriage extension or retirement extension is not valid anymore when you re-enter without reentry permit.
What can be the issue? Isn't your extension automatically cancelled when you leave the country and come back without reentry permit? You made a new entry and left legally. Why would they care about old entries? And doesn't your extension automatically expire after a year if you don't renew it? I don't get it.
The problems when leaving are normal. You should have a letter of the mother and a copy of her id card and a copy of the birth certificate mentioning the name of the mother and you. The letter should be in Thai. I had a letter in English and I had issues too.
As for coming back - they want to have you guys coming back (rather sooner than later). Nobody knows for sure, but I think you'll not have problems.
I successfully extended my visa. In my case they did not need photos. And they wanted only one set a papers(unlike with a marriage visa extension). Thank you all.