FP3 charging issues after replacing bottom module

I doubt that is the issue. Even a worn battery will charge just not much.

You can check the battery via the inbuilt system

Dial *#*#66#*#* > Service tests > Test Single > Battery Status check

You will want at least 3.8V at 50% charge etc.

You could do a spin test on the battery

Also as the charging circuit is actually on the core module ensure the contacts are clean