Anybody use a stereo amp with their ht? And ..

I don’t understand your setup.
You have a stereo integrated amp?You have a stereo power amp. and a pre amp. ( 2 units ) ?
A HT bypass , turn off the pre amp. section of the integrated amp . So only pre amp section of the HT processor is used with only the power amp. section of the integrated amp.
This is for movies.

When HT bypass is not in use, the integrated plays highend sources: turn table , streamer, tuner, CD player, R2R,
These sources sound ( stereo ) much better through the integrated amp. than through the HT processor.
This is for music.

The worst setup is having the pre amp. of the integrated amp. ´´on ´´
( no HT bypass activated  ) at the same time of the HT Processor ´´ on ´´. That way , there are two ´´pre amps ´´ that color the sound.Just my two cents .

Mine works just fine

Depends on the gear, I sometimes use play through, I use Mac. 

The cabling between the two, and the type of gear make a BIG difference.

I notice a difference, but not a bad difference. One is a C2500, and I just put a MX150 back in service. I was using a MX120 (I love the 3 speaker set up on that unit..) I didn't like the 121. or 151

If the kids come over I have a HT kinda set up.. As much as I can stand anyways. I'm not much of a TV or HT guy.. A good concert, I'm game..

Laptop yes, TV no. 30 years now.. :-) 

Regards

ht sounds are diminished after signal flows thru the stereo preamp

Can you be more specific what differences you’re hearing?  Are you using a center channel speaker in HT?  What interconnects are you using from preamp outs to the stereo pre?

If I understand well now , you have an pre amp with HT bypass.
not an integrated amp with HT bypass.( this is what I have)

When using the pre amp with the HT bypass mode activated, you should not ear any difference from the AVR  : it is a pass thru .
As @soix  wrote, the interconect cables quality between the AVR and the pre amp are important.

It is when using the pre amp. without the HT bypass mode activated that the quality of this pre amp will enhance the stereo  sound of the sources plugged in this pre amp.
The stereo sources should be connected to the pre amp.  , not
to the AVR.

I guess that the quality of the internal wire of the pre amp ( by pass wire  )   is important too.  

I run an Ayre KX-5 Twenty with an Anthem AVM60 processor via HT bypass.  Absolutely no loss in fidelity on either side (HT or stereo).  The only thing damping my stereo listening is that 65" flat screen in the middle of the room.  But nothing is perfect...