When you change the name of the Managed configuration, the mismatch alert will not find the new name and find the correct workspace and workset, even if the original workspace and workset exist in the new managed configuration.

The file was opened in Configuration "TEST" Workspace "CompanyA" WorkSet "ProjectA"

Then you open the file in Configuration "TEST" Workspace "CompanyB" WorkSet "ProjectB"

Then you rename the Manged Configuration to "TEST Work"

Then open the file with Workspace "CompanyA" WorkSet "ProjectA"

the mis alert will not find the Workspace "CompanyB" WorkSet "ProjectB", but it exist in the workspace and workset.