I got about 10 hours into my playthrough and noticed that the main building was being attacked. After awhile, I lost all input belts, pipes and combinator used for the inputs also stopped working. I tried using some repair packs and also a repair all command from another mod, but nothing seemed to help.

I love how this was discussed in https://mods.factorio.com/mod/Factorissimo2-Playthrough/discussion/60a043195403a23e8651415c as well, got marked as fixed and still only provided a possible workaround that didn't end up getting used because the player just trashed their world at this point.

Anyways I converted my file of more than 1 day of playtime and I fiddled around in the map editor a bit. I have no idea how I survived this long without the biters attacking (I guess pollution doesn't come out of the base factory of the mod?). You can just phase through the wall into the normal exit-hitbox and see the normal world, but upon doing so, the game will generate a new factory to replace your broken one. Problem is, this just takes a normal factory from Factorissimo2 instead of the one with the input item controller, and once you leave your actual factory, the contents of it are deleted since you being in that "dimension" is the only reason it's still saved (or at least it becomes inaccessible).

At first, I though this would be no problem, just slap another factory there and clone the interior of your factory before you leave it. But there's multiple problems I can't find a solution to. First I couldn't find the factory with the input item controller, so I just used a normal one and connected my resources. Then I noticed all the weird I/O problems that the mod solves by using these strange new pipes. Even if you were to do this, you'd need to cheat in new infinity chests and connectors every time your resource inputs are supposed to change. Other problems include that I couldn't get belts to connect from the outside to the inside (although I think I was just too confused and fed up to try correctly), or that you still need to clear out a perimeter of biters and set up defenses. For the latter, I found out placing cliffs with the cliff-line-drawing tool work amazingly, but spitters and worms exist. Just gotta use more cheats and create a bigger perimeter and defenses with infinite ammo/energy.

So, I found out that things don't actually get deleted once you exit the initial factory when phasing through the wall. You could just not access it, but in the 'surfaces' tool of the map editor, you can still select and teleport to the factory building. I also found out that the cloning tool seems to cause a few minor issues when copying factory buildings itself. When I had copied my base to a new building in the overworld, I noticed that the factories had been placed in the new building successfully, but had been removed from the original one. This probably happens because the buildings and their entrances are just some sort of link to the actual surface you'd enter.

Other problems I've found is the fact that I can't seem to set the player spawn inside the new factory and that every time the world is loaded now, the game will generate a new factory in the overworld and place them all on top of each other where the original used to be. You can pick up the buildings and notice it's multiple on top of each other, and you can even get a listing of all their different surfaces in the tool again.

I've also tried deleting all empty and unnecessary surfaces including the original using this tool in hopes of stopping these infinite worlds and maybe forcefully resetting the spawn location, but it seems that whenever the game is unpaused, the world will crash due to some event listeners for the on_tick method still being activated for some indecies that presumably point to said deleted surfaces.

I'm honestly at a loss. So far, I see no hope in restoring my world, which is incredibly frustrating. I'll see if any workarounds or solutions can be found in the future.

Ignore this message, I accidentally quoted my previous message instead of editing it, whoops.

Do you have resource spawner overhaul installed? it modifies biter spawns as well, It causes Biters to spawn in Editor Extensions lab when they shouldn't. So something similar might be happening here, highly recommend just turning off biters (and pollution) in map gen settings you can do this after the game has started with console commands (don't ask me how).