Welcome to the community forum.
While you’re hoping for other suggestions, I do think it sounds a lot like the USB port might have loosened in the bottom module. If you know another FP3 user or if there’s a Fairphone Angel nearby, they might be willing to let you test their own bottom module – so you could verify or falsify if it’s about the bottom module. Of course, if there’s no such option for you and you’re willing to “risk” the 20 Euros plus shipping, you can get yourself a new bottom module in Fairphone’s spare parts shop.
Your description suggests you usually keep using the phone when charging, so that might add somewhat to wearing off the USB port (respectively loosening its solder inside the bottom module).
P.S.: Actually one more suggestion – have you checked the USB port for dirt, dust, tiny hairs/fibers? Sometimes that can accumulate to a tiny “carpet” at the ground level of the port that prevents the plug from sitting in deep enough.