I've been having a similar problem, not only do I lose bass but the overall clarity drops. Sometimes my system sounds awesome other times not so much.
I believe I just found the problem, I wasn't sure if it was the amp or pre-amp so I ran the I/c directly from my Oppo to my amp. Flat sound no bass so it's the amp not pre. I wanted more volume so I reached around back & changed the input sensitivity switch, bass returned although the highs were a bit harsh. I moved the switch back & forth a few times & put it back where it was & it sounds great. Hopefully that's it & it will stay that way.
It's a McIntosh MC7270