Is a protection circuit something typically fixable, or needing a PCB replacement?
think i read in a forum that the protection circuit of the lyr 3 kicks in at any sound under 8Hz or so, maybe the cause of your problem or my input came a bit to late to help you 
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I still have Lyr 1, is there a reason to upgrade to Lyr 3?
Single Tube, easier/cheaper to roll. Has high/low gain stages. Modular expandability. Iām going to guess noise performance is much improved, and flexibility with lower impedance cans is much much better. I wonder if output impedance is lower (Itās very low on Lyr3, unsure what it was on Lyr 1). Thinking the muting relay circuitry of Lyr3 may be another improvement.
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Does Lyr3 sound better?
Thatās a subjective question that no one can ever answer for you other than yourself 
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the community feels the Lyr 3 is better. it works on fixing the issues the original and v2 has. but mm is rightā¦sound is subjective, so you may or may not like what you hear. however, thatās likely because your brain is surprised by something new / different and you will need time to acclimate and see if itās an improvement.
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Everytime I think of selling my Lyr 3, I let it warm up and plug in my Empyreans and ask myself why??
Its a really brilliant tube ampā¦
Alex
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LYR 3 now available in a black finish
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Been listening to my old pair of shp9500 on this amp. Sounds better than I remember
Hey thanks for the reply. Here I am just as long apart with my response. That makes sense, Iāll play around with trying to limit the low end reaching the amp.