See, Low Voltage shutdown Variable on ups should be adjusted the same way its adjusted once it stops charging the batteries at 14 or 14.2 Volts and the lower limit once UPS should beep and shut down should be adjusted to 10.3 Volts because if you will prolong it longer than that is not good for batteries in longer run.
If your UPS is not perfectly adjusted, you kept using it till voltage on both the batteries have reached 9Volts, which means an extended discharging during load shedding, If load is still on and its measuring 9Volts then that its self does not indicate anything like if batteries are bad or not. Yes, you are abusing it but they may still be ok. But if you have two batteries connected in series and one has something like 10.5 Volts and other has 9 then you can easily make out that it’s a weak battery. In this case, flush may work or may improve its health.
If voltage at any stage starts to drop rapidly within second like 9, 8.5, 8, 7, 6, 5, 4Volts then that does indicate a faulty battery. In order to guess a problem, you also need to compare the backup time with what it was once they were brand new.
UPS tuning should be cross verified once every year or least once you suspect a problem.