The supercap on the Vue is not normally regarded as replaceable because the PCBA is potted (unlike the VP2 SIM board). That said, IIRC there is a hack somewhere on this site where someone has managed to do it - not pretty though from memory, but guess it is inside the Vue ISS case. Also, even if the supercap is replaced, this doesn't guarantee to fix the fault - other damage could have happened.
And I wouldn't worry about the low battery warning - the key point is whether data is being lost overnight.