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Rule number one for managing map customizations is that they are intended to preserve the location of icons only in the Internet submap. Don’t customize the contents of subnets because this information is not saved. Nor are manually added connectors. Don’t assume that other customizations will be preserved. All that happens when you import a map customization file is that ovw moves icons on the Internet view to their previous locations. Any objects inside icons on the Internet submap are simply placed inside them according to the current database. Since objects are identified by their selection names, changing selection names isn’t a good idea, either.
Rule number two is to export map customizations whenever you make a change to a production map. Then back it up to a safe place. Don’t assume the nightly backup script will run in time to save your work.