I'm running 2015 SP5.0 with a PDM Standard 2016 SP3.0 vault and client

I have an assembly that was checked into the vault by another user with several references outside of the vault.

I have tried copying the missing files into the vault, checking them in and using the Update References tool to replace the files but the list of files it gives me is missing almost all of the references I'm trying to repair

Here's the list of refernces Update References gives me:

When I open the assembly and go to the Find References dialog, these are the files that are showing up

I have used Update References to locate files outside the vault and move them inside in the past but I can't come up with a systematic way of making PDM aware of the missing references.
I have tried checking the assembly into the vault with the missing references.  The missing references are listed in the Check-in dialog box but can't be repaired there.

My question is what do I have to do in order to get PDM to read these references in this assembly from files checked into the vault?