Do the actual physical beds go missing or is this something you're seeing in the Pip-Boy? Because there is a platform-agnostic issue with the Pip-Boy, where for reasons not completely understood the settlement information in the Data>Workshops menu gets out of sync. It's usually beds that go "missing" or the actual number of settlers either rising or falling so that there's seemingly more settlers than beds. Either way, fewer beds than settlers means reductions in happiness and the settlers saying stuff like what you report when you're around them.
If the physical beds themselves are disappearing, that's something else that I have never seen, and I spend a LOT of time on Spectacle Island.
EDIT: Ok, rereading your post I take closer notice of "the bed count goes red" . . .I have had an issue on the Island, since 1.4, where I suddenly lose my supply line and I have seen status indicators in the workshop interface turn red and then back again right in front of me.
Nothing like losing physical beds, though.