Hello Emu,
Thanks for the report, and the save file on the bug report.
So after looking at the data, for some reason, the water areas that you have, have an absured number of edge tiles.
The area thats trying to depelete in your save, Kisale Lake in your save has 266,179 tiles. In a new save, with the map string, the area completes as a more resonable 1782. Whats weird is that they both have the same amount of water 146,475L. So something has caused the scanning to be off compeletly, where the problems lie.
So at the point where the mod now wants to replace tiles to depleate the area, its going to be trying to replace firstly, an insane number of tiles, which arn't water, this is why its hanging, as its trying to replace a huge number of tiles, i could get it to try 3 times, but each time it'll be trying more and more as the % left decreases.
I've managed to fix the problem with the save, and ive made 2 for you, one without the mod, another with it back in, though it is on the next version of the mod 0.8.8.
Without MOD: https://www.dropbox.com/s/gdoqersuezmd2dh/Server%20Save%20NoData.zip?dl=0
With MOD https://www.dropbox.com/s/9brzdgy3zfkn2ry/Server%20Save%20Remade.zip?dl=0