Water Tiles Missing

[Rufus]

Hi!
I have this problem that when you use the "apply height: lower" tool to create rolling shores, the water tiles sometimes aren't there. This is troublesome, and I'd like to get my hands on a fix.

I flattened the map out in order to see all missing tiles, and this is the result:

This appears seemingly randomly.

Any ideas on how to fix it?

 

[Athur12A2]

I have same problem in my old project due to expanding map size after working with it for a while. Still have no idea how to fix

Off-topic: I covered that glitchy area with rocks and ruins for decorations (in middle of the sea, yes); and expand land if that area is at the shore.

 

[Rufus]

Thanks for the ideas, but I have a specific design I need to get through.