lowyhong: Uh oh. Looks like I fucked up. Any idea how to fix this?
Twilight: make an infinite well of water first... a 2x2 hole, one block deep, with water sources in two opposite corners. Then just keep taking water from that one and... umm... fill the sea with water again :D
Minecraft desperately needs a better water system :D
You are mistaken. What you suggest won't work at all.
To fix it build a solid layer one block below the water surface level (out of dirt or whatever). Any gaps beneath it don't need to be filled in--just that one layer. Once this is complete, fill in any moving areas with water from the bucket (extracting from spots one block deep for best results). You can then dig up the filler layer and the water will fill it without flowing.