I have checked both supercaps in the ISS and the repeater and they look good, no leakage.
It lost comms this morning at 4 am again, and did not reconnect until I did a Done/ -ve 3 hours later!
Pristine-looking supercaps can occasionally still be faulty after some years, so it's not a definitive test though still a good sign. You haven't said AFAICS whether you've replaced the batteries yet?
Also: The signal strength is good from the repeater, but you haven't mentioned the signal strength at the repeater from the ISS. You can check this if necessary with DIP #4 on the repeater IIRC - see the repeater manual (maybe the troubleshooting section). That said, the dropout at ca 4am sounds much more like a loss of overnight power to the transmitter either at the ISS or the repeater, so a supercap or battery issue. But always tricky to tell whether it's the ISS or repeater in this situation.