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As per this thread, similar issue
I am trying to figure out how change the "reuse modified content" box on add to workspace to unchecked by default
Have you tried setting the "Reuse Modified Workspace Content" preference to No?
Setting for yourself:
Quick Links > My Settings > Preferences > Workgroup Manager Client > Workspace > Add to Workspace and Check Out > Reuse Modified Workspace Content
Or if you are setting for site as wcadmin:
Site > Utilities > Preference Management > Workgroup Manager Client > Workspace > Add to Workspace and Check Out > Reuse Modified Workspace Content