I havnt had that happen to me (and I did play around quite a bit with the new water) so I cant explain it. But I may have a work around,if all else is OK in the scene and you dont want to lose it.
Create the water plane in a new scene (you said that works fine?) and then merge the two scenes.
(In the file command in the top menue).

"I paint that which comes from the imagination or from dreams, or from an unconscious drive. I photograph the things that I do not wish to paint, the things which already have an existence."
Man Ray, modernist painter
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