Just posting here solves my problems. That happens to me every time. I ask a question and as soon as I hit post (and eat dinner) I figure out what has gone wrong.
I have a map type and a tile type and I was changing the tile type image number and I should have changed the map type image number. So basically I was telling the game that I wanted to change all grass to ocean instead of just one grass block to ocean.
If that makes any sense... I struggled with this all yesterday and the solution was just a matter of looking at my types and seeing how they were set up. The program, as usual, did exactly what I told it to - I was just telling it to do the wrong thing.
Anyway, fixed. Thanks.