The database shows all these pieces still exist in both locations, so nothing's "lost" as such.
I'm not going to say it couldn't be an update issue, but I didn't do anything with furniture population for this one, and in the process of testing other things, I had to populate the furniture in those locations...and that was actually one of the last things I tested.
Answer this: Was any furniture showing up in either location? You were specific about the portals and chests, but there's no reason why these should be singled out.
When you went into the Angels, did you try the locked door or the public door? Only the locked door will activate the furniture, which is true for all houses. Also, if you don't have a key for the Angels hall, activating a different key will have no effect.