I think you are right here. When I re-registered in June they also told me that I should take my fingerprints again the first time I arrived back in China before the e-gates would work. I stupidly assumed this meant that I needed to use to the pre-immigration area passport scanners before trying the e-gates, which I did - and the system collected my fingerprints (but didn't ask for photo or thumbprints - I assume as these were already in the system). More likely it seems now that they actually meant one more manual entry, with fingerprint collection at the booth.

The re-re-registration procedure has in all likelihood reset the count now, so I'll have to do this all again next time I return after a trip in November!! I am moderately confident it should work after that, though more concerned about the complete failure to even read the RFID chip (on exit at Daxing), as that it is an issue that can only be fixed by upgrading the scanners - assuming that it is because the chip is buried deeper inside the polycarbonate data page compared to one in the cover (if you haven't seen one of these new-style passports you may be surprised at how thick that polycarbonate data page is ...).

Yes, that is also my recollection - but the error message that came up was definitely "no fingerprints" - so those need to be in the system at least (possibly as a back-up in case of thumb-print failure?)