When I first got Helix, I immediately loaded Ownhammer IRs, having been convinced by my reading and researching that the stock cabs were inferior. Initially I loved them, but eventually my ears started being acutely aware of the really dramatic EQ'd qualities of the different IRs. I heard exactly what you describe. After working with one for a while and dialing it in, I'd switch to another and it would sound like I was playing in a tin can. Over time my ears would acclimate, then switching would again would put me back in the tin can. It was the recent discovery that you could have IRs change with snapshots that really drove it home: I'd dial in one good sound, switch IRs and whatever else for the next snapshot and dial in another good sound, but in use switching back and forth left them both sounding hollow and "off" all the time.
So, long story short, I've gone back to the stock cab sims and haven't looked back. I've been using variations on this guys approach, which has me getting really nice results. I've posted this video a few times recently, but I think it's worth watching. It was a real game-changer for me. I recently did a full factory reset of my Helix due to troubleshooting some other stuff and haven't bothered to re-load any of my IRs. Don't know that I will.