Sorry if my english is not optimal, i speak Spanish.
As you can see there is water on top of them and the pipes on them are empty, however, the ones that aren't stay the same
As far as i know it only works on water, you don't lose any of it, it just appears on top of them
Here's the glitched save file, all tough i don't know if it's unique to this file, or is present in all save files.
First i put Sandstone Pipes on Regular farm tiles, then i deconstructed them and replaced them with Hydroponic Farms and planted Mealwood (All though i don't know if this is necesary or even matters). I am uncertain as if this bug can be replicated reliably.