You better go to your local office and talk about what you can do.
Bring fixed air tickets (an open ticket wouldn't do the trick) as proof you are not in Thailand during the application window.
- For 1-year extension application:
Some offices may allow you to apply for 1-year extension in advance when you can prove you are out of Thailand.
- For 60 days family extension:
Some offices add 60 days to your current stamp, while some set 60 days starting on the day of application.
If both are not working well for you, you have to give up the current extension. You do as you explained, or you can apply for an initial Non-O visa at the Thai embassy/consulate before you will be back.
As you are still on the first 90 days from a Non-O visa based on retirement, it's your first application for a 1-year extension. Then you will need a bank record for the full two months as minimum as of the application date. You also need to update your passbook on the day of application.
Highly doubtful that you can correct that entry stamp in Bangkok, especially with BOI OSOS at Chamchuri.
All you can do is go to Chamchuri to ask them as no downside to doing it.
If they say you can apply to proceed with an extension application with that visa and stamp, you should be fine. If they say you need to correct the current stamp to Non-IB, you have no choice other than to go to the entry point to get it fixed.
I don't think OSOS would do anything with your entry stamp.
It depends on where she applies for her initial Non-O visa based on a parent of a foreign child.
IF she applies for her visa at the local immigration office INSIDE Thailand:
She needs to have funds in a Thai bank account when she applies, means she has to have it in advance.
IF she applies for an initial visa at the Royal Thai Embassy or Consulate-General in another country: She only needs to have funds in a Thai bank account for a month (for 1st year) when she applies for an extension at the local immigration office, means she can have it just after getting an initial visa.