Use A-map 1.92 and you should be fine. 1.95 is quite buggy on all versions of the advance gen due to it being a beta. If you can't stand drawing one tile at a time and you want the new tools from 1.95, make sure that that is all you do! Set up the map and do everything else but draw it in 1.92. Drawing in 1.95 is safe, not much else.
Use the old DaN program which created it. I think you are in DNS but I am not sure. If DNS can't delete it, then switch back to DaN to delete it.
The end result is exactly what I wanted, a fully customizable room. However, it still has problems. When a decoration is about to be placed, it looks glitchy, but once it's placed, it looks fine. That's a bit of annoyance I'd like to fix but acceptable if it can't. The major problem is, when I leave the room and come back, the decorations are all gone. The game recognizes their existence since I can still put them away, but they're just...gone. Similar to when I attempted to place decorations in the non-compatible room.
Secret bases have 4 map scripts associated with them. All of these scripts use vars and cmds which have very little to no documentation whatsoever. I think these might be your problem. One of the commands is cmdA6. The only things known about it is that it allows certain tile functions to happen, such as the ash grass near Fallabor Town. Try using these map scripts on your map, they will probably help. however, the third one will need to be rewritten as it is the script for "Do you want to make your secret base here?" So, you will need to change it for your purposes.