Moving from Solidworks 2016 SP2 to 2017 SP2.

I have a lot of assemblies with virtual parts in them. I did a "Convert Workgroup PDM Files" from the Solidworks Task Scheduler.

However, all assemblies that contained virtual parts did not update. I'm left updating each assembly manually and checking them back into the vault. In some cases, the Virtual parts were corrupted (virtual part was empty)

What is the best way to get all the virtual parts in PDMW converted as well?