As in, you started a game with this mod, continued this game without it, and then wish to resume with it again?
I'm a little unclear on exactly when the various on_init and on_load events are fired so I'd have to look into that to figure out the answer. If you can share your save file that might help (and make it clear what combination of mod loading / unloading happened to get that save file).
Did you get a warning message when you tried to re-enable the mod, and what did the warning say? I wish I could print a warning when the mod is disabled but I couldn't think of any clever way to accomplish that.
The intent behind not re-enabling the mod for a save that started without is that if you have multiple concurrent save files, some with this mod enabled and some without, you can freely switch between them without having to turn the mod on and off. I guess this is less important now that Factorio tells you which mods a save file has been using, and mod configuration has been moved to the GUI instead of manually editing lua files. Also now that I am suppressing the natural water generation, that is done at startup and can't be toggled per-save, so user intervention is required anyhow. (The only way I could find to fix this would be to rewrite the entire Factorio terrain generation algorithm in lua, but it's not documented well enough for me to do that.)
If you do re-enable the mod, you are likely to have a band of terrain (maybe not visible to you yet) where normal terrain was generated.
