Steps: 

#test_1

1. place a Structure block.
2. save the structure(example E. >> for empty).
3. destroy the Structure block.
4. place water.
5. place a Structure block where the water is.
6. load structure:E
7. destroy the Structure block.

#test _2

1. place a structure block(lets call it SB).
2. place an EndPortal block or iron bar inside the SB area.
3. place glass blocks around the EndPortal(iron bar).
4. save the structure(example W. >> for waterlogged).
5. Sneak and use a water bucket on the EndPortal(iron bar).
6. load the structure:W
7. destroy the glass blocks.

Observed result: 

The water is still present and is not replaced by the structure:E(W).

Expected result: 

The new structure should replace all the blocks.

NOTE:

related to MCPE-115971