I have checked the FP3_flashall program and it should not touch the modem1 and modem2 partitions which afaik contain the IMEI information.
You could try to enable ADB debugging, maybe there are some errors in the logcat which could help to identify this?
Or try to install an older manual installation image, e.g. this one for A.0120. The link for A.0134 does not seem to work anymore but I could try to upload FP3-REL-2.A.0134-20200703.120010-user-fastbootimage (2).7z if needed (but this will take a while).