Thanks for the suggestion, but nope... not using passenger mode here.
The good news is that I know how to reproduce it now. It seems if I set up the headset from a hard reset on the downstairs floor, everything will work correctly until I move it upstairs. When I move it upstairs, it reports that it lost the boundary, and asks me to reconfirm the floor and boundaries. So far, so good... I reset the floor and configure a stationary boundary, and everything works correctly on the upstairs floor. The problem seems to occur after that.
Once I have configured it on the upstairs floor, it doesn't seem to ever lose the boundary again, and instead offers to switch to "room scale" with a button. Even walking entirely down the stairs away from the upstairs area, or powering it on to start downstairs seems to result in this behavior. If it only offers to switch to room scale rather than reporting "boundary lost" it doesn't appear to reset the floor correctly for many VR apps, even if you go through manual floor and boundary resets in Settings. After manually resetting floor and boundary in the downstairs area, it will result in the Lobby, VivePort, MR apps, and Steam apps correctly identifying the new floor position but any local VR app (Wolvic, Virtual Desktop, any game, etc.) will have the floor position up about 12 feet, at the approximate level of the upper floor.
I've managed to get it to force the "boundary lost" message by wrapping the entire headset in a blanket, and carrying into a dark bathroom and shutting the door. Then it will spin for around 2 minutes after unwrapping it and putting it on my head, and report "boundary lost". After that as long as I manage to click on the "OK" button before leaving the bathroom, I can reset the boundaries on the lower floor and it works correctly (until the next time I move it upstairs). If even the bathroom door is open, or I don't click on the "OK" button for the "boundary lost" popup while in the the bathroom, as soon as it catches a glimpse of something it recognizes outside of the bathroom door, it removes the "boundary lost" message and re-establishes the existing boundary with the bugged floor position for most apps, switching back to "return to play boundary" message with an option to redraw the boundary with a "room scale" button visible.
Really frustrating bug, and I hope this description will help the Vive team figure out how to reproduce it and fix it. Or at least give us a manual option to reset the boundaries which functions the same as the "boundary lost" message, which seems to do something different than the reset options in Settings currently.