Hmm, I have started from scratch with my own FP3 once again, following the same official Fairphone guide you referred to and installing a newly downloaded “FP3-REL-Q-3.A.0045-20200905.155001” plus installing my own system.img according to my own instructions - all from Debian/Ubuntu and all as I did before… As a result, I was able to reproduce your issue: The fingerprint sensor doesn’t work now although it did before. At the moment, I have no clue why. It might be related to the (random?) issues others observed with the current Android 10 vendor firmẃare (Android 10: no fingerprint for unlock or FP3+No Fingerprint after restart). But before taking any conclusion, I would like to cross-check with some older builds of mine. Unfortunately, I can’t do this before Tuesday - sorry for the delay.
BTW, please feel free to report any issues at https://github.com/fwg-cag/treble_build_los/issues, however, I’m not in a position to guarantee you any support or quick resolution…