Update #2

I was able to reproduce the issue fairly easily in WebOrder sample. Just added a new common table as parent for both OrderHeader and Inventory table.
Which is pretty similar to the simplified DDO structure I posted in my first post.

And was able to reproduce the issue. The parents of the constrained-to table is being cleared as part of the child ddo clear operation, which should not happen.

@ DAW, I have created HDE ticket 6715 for this.