Hi TGxAssassin,
This issue is one that’s known by the team. I’m sorry to hear it has affected the base parts in your save. Those affected have reported that it seems that if base parts are only joined by one side, they can be broken down, but when joined by two or more sides this support error appears. I have a Known Issues post on this here: [Known Issue] Deconstruction of raft bases
Some players have found that trying to break the base part from underneath has worked for them. However this involves flipping or lifting the raft, which I understand with a large raft may be difficult.
I’ll add your details and image to my report on this issue for the team, and also note that you’ve experienced the issues with the crates and being unable to break down the shelves on the same raft.