Hi @FeelsGoodman124 :)
I tested the mod on all surfaces (planets) in Vanilla Factorio, and there wasn't any issue with creating unwanted tiles (like lava or ocean).
Is there any chance, that you are using other mods, that are creating non-standard surface (planets) or non standard biomes (lava, etc.)?
Don't worry, my mod doesn't change the "crater generation" or the whole savefile (or map).
This is how the mod works:
-) It searches for burned tiles (nuke scorch marks) and nuke entities (craters) in the given radius (default 50 tiles radius), other craters are not affected
-) It deletes the craters (again only in the 50 tiles radius, other craters on the map are not affected)
-) For the burned tiles (brown spots) it's more difficult, since the ground tiles are replaced by "burned tiles", so there is no way to "just" delete them or revert them (because the previous tiles have been replaced by "burned tiles" and now the map only contains the "burned tiles")
For this reason, the mod needs to re-generate the missing tiles. This is how it works:
-) It takes the "Map Seed" you started your playthrough with, and it generates new tiles based on your "Map Seed" on a hidden surface layer
-) The reason is simple. The same "Map Seed" always creates the same "Map/Planets"
-) So by doing this I know, what the original tile / surface / planet looked like, and I'm using the original tile of the hidden surface layer
-) I only re-generate the tiles that are needed (so I don't re-generate the whole planet or surface)
-) Then I copy the newly generated tiles from the hidden surface to the current "burned tiles" and replace them
-) Afterwards the hidden surface is deleted again (so it doesn't increase the savefile size)
So, as long as you are using Vanilla Factorio, the re-generated tiles are always exactly the same as it was before:
-) Meaning if there was grass before the nuke, then after the re-generation, there should be grass again
-) If there was an alien biome before the nuke, then after the re-generation, there will be alien biome tiles again, and so on
But it looks like, this doesn't work on your savefile, so there might be some reasons for this:
-) There is a non-standard Map Generator Mod installed
-) There is a non-standard Biome Generator Mod installed
-) The Map has been edited (in the Map Editor, or by a Mod), so the "current" tiles, are not the "original" tiles
-) Or any other reason, I cannot see right now
Regarding your question:
-) Is there's any way to fix my savefile that permanently has this mod's version of the craters?
Since your craters have already been replaced by the original tiles of the savegame (based on the Game Seed) by this mod,
there is no easy way to get the previous tiles of your savegame back (because the mod only knows what the "original tiles" looked like, not what the "previous tiles" looked like).
There are two solutions:
-) Use the In-Game Map Editor to re-create the previous tiles (manually yourself), if you noticed this behaviour recently, there should be many craters you have to edit manually
-) Use an Auto Save to revert back to the original SaveGame (I can see you posted this question 6 hours ago, so maybe you still have an Auto-Save without the modifications)
So my questions are:
-) How many craters did you replace? This mod does not automatically remove craters, only when manually placing Ghost Tiles, so I assume you did notice this behaviour early, and therefore not many craters are replaced, correct?
-) Do you use any mods that change the Map Generator, and/or Biome Generator?
-) Are there some mods that change the Planets/Environment?
If yes, then my mod is incompatible with your installed mods, because my mod only uses the original tile from the Official Map Generator.
This mod cannot re-generate tiles based on other Map Generators, or Biome Generators (I only use the Official Map Generator, to generate tiles).
So, if you want to keep your mods, and you still want a mod that removes the Nuke Scorch Marks, you can try the mod by Sil3ntSt0rm (his mod doesn't use the original tiles of the Official Map Generator, instead he is searching the closest tile and copies/duplicates its values. So you will not get back the same Terrain/Environment/Planet as before (aka. the original savegame tile), but it will be filled with surroundings that are closest to the nuke. So in this case, if you have grass tiles next to the nuke, the whole nuke will be filled with grass tiles. It's a different approach, and you will get different terrain/tiles as before, but this will solve your problem if you have mods that change the Surface/Planets, or if you use non-standard Map Generators, or Biome Generators).
Hope this helps :)