This is why contractors charge a lot for permits. I’ve pulled several permits in the past year and I’m beginning to learn what to look for in plans that might cause red flags. That said, I’ve never been asked to mail certified letters!
When I’ve had to re-submit drawings, they’ve just been appended to the original application. You may need to go to the file room at dcra and ask them to give you the application and plans back (or to find them if they’re sitting on someone’s desk), but then you can change the plans without losing anything that’s already been approved.
It sounds like you’re getting some strange advice. I agree with the person above who asked about the homeowner’s center. This should be a pretty minor project, and they’re super-helpful there.