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How did a successful HUB server upgrade to ND6.5.1 turn mutant?

Our global infrastructure is R5.0.11. Two days ago we upgraded our HUB server to ND6.5.1. Generally, we haven't had problems. This afternoon, however, the design became a hybrid of R5/ND6, and we can't work out where this came from. We have checked the obvious replication history, but can't see any reason why the design should become partially overwritten. Any suggestions?
I have no immediate answer without looking at the database in detail. For starters, you can look at the offending design elements. Check the modification dates, last editors, design template and the various design replication options.

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