The OP says the floods are bugged, as the halfed mp and inability to build forts/watchtowers remains permanent, though that is not entirely true.
It is possible to unbug it. There is a "working" example from Westeros Total War (they use it for Moat Cailin region)
Code:
event flood
frequency 1
winter false
summer false
;warning false
position 74, 204
position 64, 202
position 61, 195
position 73, 191
position 70, 194
position 81, 141
climate swamp
;climate unused1
min_scale 2
max_scale 5
Im not sure if they knew about the bug or not... its possible they knew, but they didnt mind if it happened, as Moat Cailin is supposed to very inhospitable.
Anyway, as this flood disaster is very frequent (the mod has like 2 or 4 TPY, so it happens quite often), after a few turns it is going to happen at the same position again (each time the disaster happens, one of the positions is apparently randomly picked... though they are all in the same region, so seemingly not much changes, except the position of the visual flood, if you can see it).
And when it happens again at the same position, it gets unbugged! After the second flood at the same position the movement points are restored, and you can build forts/watchowers again, I tested this
.
So I think the OP should change, as you can use floods just fine, but you always have to add a second flood shortly after (unless you want a specific region to be "inhospitable") at the same position. Of course, this happens only to the affected region.
(A funny side note, how I came to testing this... in a hotseat we struggled with endless "storm" in WTW.. suddenly all ships lost half their mp, and it lasted for many turns... However, as the storms are disabled in WTW, I eventually found out it must be actually caused by a bugged flood... and indeed, the last position in the sample script I show above is supposed to be in a swamp, but its actually in a sea river, therefore in sea region. And hence the same bug applies, but only to the sea region this time... and it gets unbugged the moment the flood happens in the same sea location again)