ED visa, Medical visa and Myanmar workpassport question

I wrote in an earlier thread that my wife did not get an extension due to attending the wrong class at university. She is currently on a 3 months Medical visa that expires 26 september (just had a baby) and now the question I have is the following.

She will obtain a " temporary" workpassport of the type that is between Myanmar/Thailand, it will be issued in Bangkok with stamp from immigration and all so she actually won't have to leave and re-enter. Will it be possible to somehow stamp the permanent passport so she can end medical visa in time and not get in trouble for overstaying on it, or will she have to exit and re-enter on workpassport. The problem I see is that she will have two different passports with stamps in them, so she will actually need a re-entry stamp for workpassport.

An option is to go to Yangon end get another ED-visa, but I arrive from offshore on the morning of the 26 and with a 6 week old baby there is no way she will leave without him going with her. I will then have to rush to Myanmar embassy and get same day visa for both him and me so we can leave on evening of 26 september. As you can see it is a timeframe I would want to avoid if possible.

Hope I did not confuse you to much as this is complicated even to write correctly.