I used to find the trees in my rooms would delete if Moo was not enabled when placed if they were in a medium height wall room to accommodate their height but I am placing them in a level with short/standard height walls. If memory serves the fact that when I placed the room it forced my tree room to standard height so the roof deleted the tree. I could work around this by enabling moo before I placed the tree room.
Another workaround I do now with all of my plants that addresses this tree issue far more easily is I save them in a room that I have deleted the walls from, and I make sure the ceiling is deleted also. I do this in the yard. The plants or tree need to be in a planter/pot, and I do not delete the floor tile, so it still registers as a room when I click the floor, and I can save as a room. (The reason the rooms in these screenshots look like they have grass is because I used the grass-look floor tile.) Or I suppose you could just delete the ceiling. For example, this is how my tree/plant rooms look in the library or gallery:
Also, I seem to vaguely remember that maybe if a tree got deleted due to the room wall height when I placed it on another lot it may have turned up in my household inventory? Do you see your tree in the household inventory by chance?
I would love to also hear any results from testing if there is any content in your planters that you're not seeing, per the recommendations @PipMenace made. I never thought of checking for that!
