This just happened to me 1h ago.
Used the level 80 boost to free up the shared inventory slot and get the items while I'm at it. I was using Runes X on my original ascended armor. Got a ton of new Exotic armor that I trashed (no interest in it, having an ascended set with build-relevant runes on it).
Afterwards, I notice the runes on the original ascended set have changed. Not the armor pieces (same skins, and same stats), just the runes. A whole set of X is now a full set of Y.
I'm ready to re-buy the runes from the TP and admit my error if somewhere in the boost dialog pop-up there is a mention of this behavior (which I find no justification for, and doubt anyone reasonably assumes this will happen). So, has anyone SEEN a warning of sorts?