This happened to me before, and I thought I was imagining it, but it happened in front of me, so I knew I wasn't losing my mind.
Scenario:
I was making multiple profiles of a George Lynch Super V (Modified Vox).
After finishing profiling, I went to browse mode.
I was testing the profiles I made, and there was one that sounded harsh to me: profile #14 of that session.
I went to profile #15, and it sounded much better.
I then selected profile #14 in RM, single mouse click, without changing the profile (still #15) on the profiler.
I right clicked and selected Delete Rig on the popup menu.
At that point, both the RM selected rig (#14) and the rig on the Profiler (#15) were deleted.
I know this is an ID-ten-T user error (developer humor). But is this the expected result?