What should happen when the “parent” duplicated question is deleted?

A possible solution would be to see duplicate questions as a linked list or a tree. We then can add rules:

1. if question X is marked as duplicate of A and A is already a duplicate of B, mark X as a duplicate of B.

Before:

X A -> B 

Try:

X -> A 

After:

X -> B A -> B 

2. if question X is marked as duplicate of A and B is already a duplicate of X, also mark B as a duplicate of A.

Before:

B -> X A 

Try:

X -> A 

After:

X -> A B -> A 

Now each chain/tree of duplicates always have the same root.

If we now try to delete the root, two things can happen:

1. All questions are deleted
2. The root is protected and can't be deleted.

There should be functionality for moderators to change the root in a chain/tree, if another question has a higher quality.

If SE doesn't implement any changes to the system (like the one proposed by Gamecat above), then we may have to make a new policy.

I propose this: Whenever the last/binding delete vote is cast on a question, the mod/user casting it must search for dupes. Searching for dupes is easy enough, one can just use search with the closed:1 parameter. Even better would be to use URL search, but it's not working properly at the moment. The sidebar "Linked" list, as mentioned by BenBrocka below, usually has dupes as well.

Then, these questions need to either be deleted or reopened (depends on the question). Of course, that's a logistical nightmare unless you have a diamond mod around. Or, if enough dupes exist, it may be better to just not delete (again, depends).