With the volume of files you are talking about, it may be worth while to write an application to update the references.
If you really have only one file that you want to fix, you could add that file's directory to the list of Referenced Documents in the SW settings:
Doing this will ensure SW will always open this master file even if the assembly is referencing the file from another location. Over time, as you checkin assemblies that would now reference the correct document, the problem will eventually fix itself.
"Time heals all wounds"
I'm not in love with this solution, but it is a very cheap and easy fix.
We are having issues when migrating Assemblies from a network drive to the Vault, where the Assemblies once Checked In are still referencing files on the network drive. If the same referenced file exists in the Vault will placing the directory in Referenced Documents "force" the Assembly to reference the file in the Vault? Will it include sub-directories? What is the difference between this setting thru SolidWorks and the "External Reference" setting in the Vault as shown below? THANKS.
I haven't messed with the referenced documents idea... though that seems problematic to implement on a system-wide basis. Could that be used at a directory level to, say, put all commonly referenced parts in one folder, and then point the referenced docs at that folder to force all parts to use the standard parts in that directory?