I checked again. Both PLLs unlocked overnight. The laser temperature drifted down for the ppol (maybe 50 MHz equivalent) and also down for the CC (again maybe 50 MHz equivalent). 

I relocked both of them. The ppol one had a bit of weird behaviour where it does some kind of twitchy unlock relock behaviour - it skips maybe one MHz away from the lock point but then is quickly caught again. I reloaded the PLL settings (Analog Devices ADF4002 SDP board black) and turned on the Charge Pump Gain setting. I'm not entirely sure if that fixed it but I left for lunch, came back to TAMA 90 minutes later and both PLLs were still locked. Maybe I can turn up the timeout delay on the ppol too. I think fiddling with these settings too much may change the phase noise but I will check that after I recover squeezing. Perhaps there could also be a bit more optimization with ppol mutual polarization matching and laser to fiber alignmnet but for now it's serviceable. Anyway at the very least I think I have confirmed that there is no major stability issue with either PLL loop on its own. Now we see if that is maintained for CC1 and CC2 on squeezing.