My question is, could the ~4v inputs be responsible for damaging the pre-amp tubes?
In the first 12 months one of the PL tubes started an intermittant high pitched whining. Swapping tubes one by one from left to right channels isolated this, and replacing the tube fixed the issue.
NO, absolutely not. Your tubes are not getting damaged by input level. In these cases either the tubes are going noisy on their own, or the amp design is very sensitive to noisy tubes. So the Prima Luna’s sensitivity of 415mv indicates a gain of (calculating...) 37 dB!? Holy cow!! I’ve NEVER heard of an amp that high. No wonder. That means the pair of 12AU7 for "input" slots are under a sonic electron-microscope (so to speak), and need to be EXTREMELY low noise - and stay that way, over time (that’s the bugaboo). (EDIT: I forgot the 37db is from adding "line stage" gain to power stage gain - it's OK then, but still reasonably high)
If you see tubes graded "MC phono grade", that’s what you need here. Frankly, it’s almost baffling for an amp to have this much gain. The most I’ve ever had is 33dB and even that seems crazy at times.
Adding attenuators before the Prima Luna (adding after is a big no-no) will NOT help your case here. The amp’s volume control should be positioned BEFORE the input tubes (as in 99.9% of all preamps), which protects them from overload by input signals - BUT the downside of this is that you get to hear the amps’ "full gain" at all times. That means tube noise issues are made readily apparent, and if your speakers are sensitive you’ll hear lots of hiss noise floor too. If you have channel imbalance issues from the potentiometer tracking at low levels, then the attenuators can help with that - but not with the noise.
So if an integrated amp did place the volume control after input tubes, then your noise issues would be a whole lot better - BUT now you could easily overload the input stage (especially with modern DACs), and that will make your sound have lots and lots of crunchy distortion.

