Building Gadgets Version
1.3.8

Describe the bug
Exchanging waterlogged slabs and stairs will cause the block you are exchanging to be voided, I suspect this may happen with all waterlogged blocks, not just slabs and stairs.

To Reproduce
Steps to reproduce the behavior:

1. Place a slab down
2. Turn the slab into a waterlogged block by right clicking it with a water bucket
3. Try exchanging the slab for something else such as planks
4. Notice slab has been voided

Expected behavior
The block you are exchanging to not be voided

Issue originally reported to FTBTeam/FTB-Modpack-Issues#6894, also tested it in a quick pack that only contained building gadgets

This issue also occurs with waterlogged and lavalogged Mekanism machines. When I tried to exchange the machine for another block, although the fluid successfully returned to a bucket, ‌the machine itself was not returned and was lost‌.
Building Gadgets Version 1.3.9

This is an NBT issue. The waterlogged block has an NBT tag for it's waterlogged state but that block does not exist in a player holdable item so the game cannot give it to you. Would have to be stripped of the NBT tag to render it back to just a slab so it can be put in the player inventory. Not sure if there is a way to transmute the item while "in flight".