Like Sidmarill said, if your structure already has mods in it it will remove the mods. But as seeing you are in vanilla, you could use the worldedit mod to make changes and than change it back to vanilla, it will warn you if you leave a modded block it's missing these and make a backup of it, but backups are always a good thing in the first place. And even though you are probably in 1.12.2 the mod for 1.12.1 should still work. Hope it all helps.
You only get that missing mod warning if you open the world in Forge without the mods - vanilla does nothing at all except crash or regenerate the offending chunks in the worst-case (just some unknown blocks usually doesn't cause any issues other than disappearing); for example, the following happened when I intentionally opened a modded world in vanilla, there were no other indications that anything was wrong:
However, if only vanilla blocks (items, entities, tile entities, biomes) are present it is perfectly safe to open the world in vanilla unless a terrain-altering mod was used (there will be discontinuities between new and old terrain, as with upgrading from 1.6.4 to 1.7.2, otherwise it is still safe to open it in vanilla, unknown biomes will also just default to plains but that could cause undesired effects).
Also, I personally recommend using MCEdit since you do not need to install any mods along with the potential issues using mods can cause, and MCEdit is capable of performing extremely large operations with minimal resources (for example, I've used it to analyze a 90,000 chunk world on a 32 bit system; that many chunks requires on the order of 5 GB of RAM to load all at once. It will run slower though due to disk caching). MCEdit is also able to open worlds created in almost any version, even ones released after it was released (as long as the save format remains the same, this is likely to change in 1.13), as well as virtually any mod (again, unless they alter the save format, such as Cubic Chunks), although there may be issues with some blocks (e.g. an unknown light-emitting or transparent block will be treated as if they do not emit/pass light since that properly is inherent to the code, not the save data).
To remove water lakes you also need to edit "generatorOptions", which for Superflat worlds is a string which includes all the options, with lakes being enabled with with "lake" and "lava_lake" (I'm guessing that you used the Overworld preset, which has both with water lakes being much more common).