I know that Oda already made something similar happen but could it be a logical flaw? I also know that a similar question has been asked but nobody answered anything relevant to what I wanted to understand.
Not at all.
Being in seawater or exposed to seastone doesn't change the physical make-up of paramecia type devil fruit users it merely incapacitates them as demonstrated when Luffy was immersed in seawater during the Arlong arc, while he was unable to move his neck was still able to stretch allowing Nami to hold his head above water.
By that same token Brook wouldn't be able to make any active use of his abilities but he'd still stay in his undead state.