Wow, you certainly do have a lot happening right now. o:
Hopefully some these things can fix the issue ( as I have had similar issues myself when I was making maps ).
For starters, make sure that your computer didn't move ANY of your files.
Sometimes during updates, the computer will move files around the computer or even get rid of things that's not supposed to be removed. It happens to the best of us and it can't be a little frustrating but make sure that everything, is in fact, still where it's supposed to be.
Make sure that it isn't a rendering issue.
I think depending on certain rendering systems, certain items would show / not show currently in a map. I think that happened once or twice for me and I didn't understand why only some things were coming up while others weren't... So I won't count that as a missing file or anything.
Try backing up all your files and then uninstall FH completely and add a couple things in at a time.
I know this one is a bit tedious and I usually use this as a last resort in case it isn't my game itself that's giving me issues. I believe I had to do this a couple of times or so just to be on the safe side and it's worked thus far. Like I said, this should probably be used as a last resort amongst anything else.
Try removing the specific item that's missing, save the map and then add it back in again and check to see if the problem persists.
Sometimes this does the trick for me. Simply adding / removing objects just to be sure it's not just some silly glitch on my end. Try having someone test the map out as well to see if the problem is one sided or not.
Double Portals.
I'm not entirely sure why it does this for me as well, but I think when my friend was testing it out, it would either be there or not so I'm 5O / 5O with this issue. I'm gonna have to do some further investigation unless someone knows the answer to this. But it still works no matter which Portal I run to.
Hopefully something gets sorted out though. I could be overlooking some things or getting some issues mixed, but this is just solely based on my experience and not everyone is the same way. Good luck o: