I noticed in VEE, that Dev Tools -> Find External References's popup warning is the same as the one for Check ALL Events for Errors but it probably should be the same as Find Related Events.
Unless the warning is correct and it's implicitly running a Check ALL Events for Errors as well? It didn't seem to change any file times for the .ve.xml files, so I assume it didn't resave the files as the warning claims.
Fixed, was wrong text as you assumed.