Fairfield reported this and I've replicated the issue on the very latest code.
When deleting & transferring references at the Lot level, the object relationships are not transferred.
This appears to be intentional as there is now warning text that states "If you continue this object will no longer be associated with a Lot." This is apparently contradictory because the "transfer reference to" lookup still allows the user to retrieve and select another lot to transfer the references to.
Can the original behavior be restored?
The message about references can also refer to all of the other relationships a lot can have (to entities, collections, etc). There was a reason why we didn't move objects along when a lot was deleted, but I can't at all remember what the reasoning was. I agree that it's confusing as-is and that it makes sense to move them as we do all other relationships. The change to do this is in GitHub/develop.
Just tested this and it works. Let's give CTCO the change when we're adding new databases tomorrow. Thanks!