When broken data sources for coverages are repaired in the map document, all coverages in the .mxd are unexpectedly set to the same data source, including those stored in different workspaces.
Set the data sources individually for each coverage dataset. This can be time consuming when dealing with lots of coverages and lots of mxd's. Another potential workaround would be to set the data source for the mxdthrough ArcCatalog using the “Set Data Source(s)” function. Users must save the changes to a new (copy) .mxd otherwise the new file paths are not retained in the orginal map document due to NIM005064.