Question (maybe a silly one):
Do you have the speakers connected with to pairs of cables from the correct terminals on the back? (I'm assuming you do)
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And do you have the "bridge" on the back of the speakers disconnected? (those fancy turny knobbies must be turned counter-clockwise to unlink the Hi and Low drivers)
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This is simply to ensure that the Bi-Amping was set up correctly, but I assume that's what you did.
Why am I asking?
My Suspicion is, that you are hearing only "part" of your speakers when your issue arises, with the receiver somehow disengaging the bi-amp mode.
In order to identify this problem, I would suggest rolling back to non-bi-amping (there's really not much use in bi-amping here, even though the receiver should be capable of providing more power that way, you won't gain more than 3dB headroom anyways.. and we're talking way beyond 100 dB here already)
Suggestion:
1. Reset the Receiver and start from scratch. Connect the speakers without bi-amping
Link the bridge on the terminal of the speaker, only connect one cable, disable "bi-amp" mode.
don't run any room correction (not much is active in direct mode anyways) and don't set up distance and EQ and crossovers yet.
2. Test it this way. If the issue doesn't occur, then re-install the bi-amping, unlink the bridge on the speaker, connect the second set of cables, activate bi-amp mode.
Still no room correction, no EQ, etc. just switch to bi-amp mode.
Now test again with your music.
If the issue occurs, there might be a problem with the software and the bi-amp mode.
Install the Pioneer Remote app, but also check the display (not the big letter stuff, the TINY symbols along the edge, gotta get really close to see them, like 10" away)
What does it show. Does it really list Direct mode when the error occurs? Or does the mode switch to something else?
TLDR:
I wouldn't use bi-amp mode with any AV-Receiver. Your problem probably goes away if you simply don't use it. 5 Minute fix.
If you have an hour, try my suggestion above, before requesting a warranty replacement.