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You may be prompted to check out a read-only/checked-in XSD file that is under source control whenever an attempt is made to modify the XSD file opened in the XML Schema editor. However, if the changes are made in the design view, then the changes are lost upon save. If the changes are made via editing in the source view, then the changes are saved.
Workaround: Check out the XSD file before making any changes to the file in the XML Schema editor.