Actually, zeroing out the encounter rate doesn't stop encounters. The game has code which checks if it is zero, and sets it to a base value if it is. So there is ALWAYS a chance of an encounter if there's Pokémon data.
If you don't have a Water section on the map in question, it's not exactly the worst thing just to leave the data there, it simply won't get used. If you DO have a water segment and need it to have no Pokémon, it's possible to remove certain sets of data by (this sounds utterly counter intuitive, but bear with me!) hitting the expand button. It'll open up a dialogue for you to choose what types of wild data you want. Simply uncheck the relevant one, and press OK. This will safely remove the wild data from the map. (This is on A-Map 1.92 - not sure if it'd work on 1.95)
There is a still better way to do it, involving hex editing, if you're willing to do that. Do everything you did last time up to the unchecking in the list. Instead, take note of the first valid offset in the list, convert it to little endian (reverse hex) and then search for said offset in your ROM. It will lead you to the pointers for your map's wild Pokémon. Now you can zero out any unwanted sets of map data from the map without repointing the wild Pokémon pointers (which is what method 1 does).
As to changing the old ones back - Try using method 2 to find the pointers and see if you have an invalid pointer in the list.