Maybe you want to read on here.
So I assume if it’s not mechanical as you have already switched the top module there may be even more circuitry for audio on the core module. Maybe a #fairphoneangel is in your close vicinity to have both of your modules tested. If they remain to work then some of the other audio related circuitry on the core module may be damaged.
Specifically these cracks should be avoided. (no matter on which device! I blew my filter that way on my PCs audio input line). Actually these are “signal peaks”. Depending on how well and robust the protection/filter circuitry is designed in the phone it can handle those peaks more or less well until being damaged.
If one take a very close look at how these audio jacks and plugs are designed (2,5mm, 3,5mm, 6,3mm any) and slowly joining/splitting them (can be examined on the pcb type or the type being screwed into cases as they are usually not fully encased) he/she should realize that there is a position where two contact are bridged (actually shorted). So how good is it for an audio driver to be shorted on his output…?
Also grounding is provided on this plug type at last. This is very old, but anyway not really made for hot-plugging, technique. It should always be dis-/connected without any signal on the line. Professional equipment therefore usually have XLR connections in use (many [acoustic} guitars may still have these conventional sockets built in though). Grounding/hot-plugging with XLR is properly assured.
It sounds trivial, but now you know there is something wrong.
Another example proofing it’s not hot-plug save:
My girlfriend’s Panasonic DECT phone just as mine has an audio jack for a headset (mono speaker, but stereo plug for the mic signal line). Keeping it attached just for moving it to get charged was sometimes uncomfortable for her, hence every now and then detached. No one knows when the next call comes in. So calls were taken without headset for being plugged-in shortly after.
This crackling noise was heard but all went good for some time.
But one day the audio driver gave up while plugging-in and there was only very little noise to be heard, not of any use for conversation anymore. She had to replace the phone and has learned her lesson.
Maybe not quite I guess. Bluetooth may use completely different routes to the audio processor than the hardwired socket. But you can test if audio output in general still works.