Resurrecting this old post I did back in 9.1 days. Looks like same issue exists in 11.1. In my current case, I have a bad Part that a user did a save as on and I want to remove. It was called by a released assembly but by older iterations. The problem is we use View Versions and the iteration exists after the branch was made to the view version. There are 150+ iterations I cannot purge because of this and therefore, I cannot delete this part. It past conversations with PTC they indicated fixing this would mess up BOM integrity but I cannot see how. I know of others who figured out a DB hack to clear this but not willing to do that. Perhaps I will repost to enhancement requests.
Summary: Ability to purge older iterations of Parts held only due to branch dependency. Suggestion, alter branch point to latest iteration of the version that was branched off of.
It does look like the same limitation exists, and it seems specific (like you mentioned), to the branch point iteration (and affecting iterations after that).
There is this product idea I was able to find:
Which is specific to your need, I believe. It seems like, the WCTK healer that is mentioned in that product idea thread, can be utilized to accomplish what you want.
I would suggest opening up a Support case, to get a fresh look at your requirement, but it seems like others have utilized this:
Again, I would suggest consulting with Support about this first.