Much delayed, but just to add for future readers if nothing else that the linked mod replaces files in the game's Content folder. There are much better ways of modding than just overwriting files,
which has many disadvantages compared to even the most basic content pack for SMAPI. In this case someone did
convert it to a basic pack for Content Patcher, which you'd just drop in your Mods folder.
(It's worth mentioning that even the conversion is not ideal, because it still just replaces the entire file even though it is only really editing the lake, but it's probably a big enough change that it's not that big of a deal. And even if it was, at a bare minimum it's easier to install, easier to keep installed when the game updates, shows up in your SMAPI log, etc!)
To expand on what Odin said on the changing maps mid-save response, when you make large changes to a map you can end up with things like buildings in the water, misplaced debris on cliffs, that kind of thing. It's not game-breaking and it's generally okay to switch and see how it looks to decide if you want/need to move some of your things. It's not likely to cause actual gameplay issues unless maybe you go from a giant map to a small one or something

(And even you have problems, you can just switch back without saving!)
Mods like
Reset Terrain Features and
Crop Transplant can be really helpful for tidying up a map after making big changes, but as Odin mentioned since this is just removing the pond it shouldn't be a problem at all.