Yeah I have. Just did a shell swap for my DS Lite and the donor unit's shell had the same thing with the bit of plastic as with your red DS Lite.
There was another difference I found during the shell swap, and (at least in my experience) both shells used different barrel hinges. When I tried...
I'm surprised you got that to work. I used to think that they checked if CFW was ever installed on a unit at all, but it looks like they only check if CFW is currently on a unit as long as it can boot.
Do you have the details of the new SD card you're moving to?
And just to make sure, can you show what the root of both SD cards looks like (e.g. screenshots)?