Well, I guess that's part of my interpretation as a bug: one of the supposed Pro advantages is the unified view of your devices. If device A (PC) is linked to B (phone), and then B is linked to C (PC), it should work, even if A and C share a folder from before. And according to my reading of the link you provide, it is a supported mode of operation. But what's undoubtly a bug is that B is forgetting A when C is linked. (Also, C doesn't add A through its linking to B as a known device).
In regard to the "(1)", this was a folder in A, already known by B (through linking with A), with same key in C (through manual key passing before Pro). I don't think B should interpret it as a new folder from C, since it has the same key that it already knew? Although I see this is a known "feature" based on the link you provide. To me, it's related to the previous point in that B doesn't simultaneously remember A and C.
Thanks for the feedback. I will try to restart the identities and linking from scratch to see if things work out.