Creatures Caves

Nope, deleting the agents file won't help.
Also, in theory you have to inject the remover agent, i.e. hit the green button, not the red one. Some remover agents also work with the red button, but by default you should hit the green one.
Also, red-buttoning the metaroom itself generally is a bad idea. It will most likely just delete the individual objects it installed, not the room itself.

Most people probably do not make remover agents or just sloppy ones because they are tedious as hell, about as much as the room itself, maybe even more.
- First you must remove all the native agents.
- Then you must make sure there is no other "immigrated" agents, such as other plants or even creatures, yet have to make exceptions for stuff like the HUD. Just one single little object, like a seed for example, could ruin everything. The default solution is to teleport everything somewhere else, but even that is risky, as the objects might be e.g. unexpectedly large and cause an error upon teleporting. Killing the objects might be an alternative, but is dangerous too. What if you hit vital parts of the ship/game by accident?
- Once you somehow actually managed to empty it out, you have to delete every single darn room it has. With "room" I mean the little cells that you see with dmap 1. You have to remove each and every of them individually. This can be done by a loop. The other problem is that they get their IDs dynamically assigned. To name an example: when you first inject chione and then NG1, then chione will have completely different room IDs than the ones it had if you injected it after NG1. This means a big lot more work to find out which rooms to destroy and which not.
Alternatively you can just save "your" IDs upon creation, but then you somehow have to get them out of the list again, which is annoying too. Not everyone might come up with this idea either.
- Lastly you have to delete the background art and unregister the metaroom itself. Actually it is fairly easy, but you must go through all the other steps to safely get here.
Oh, and during this step, not only objects are forbidden in the room, but actually being there with the camera might cause chaos as well.

Also, if anything of this causes just one teeny tiny little error, the entire stupid script gets cancelled and you end up with a half-destroyed, messy something that used to be a room. Yay.