Have you tried to use Thinapp for the software? Maybe that will allow for you to retain those settings that are unique per user. If that doesn't work then it sounds like maybe your use case calls for full desktops instead of linked clones.
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Have you tried to use Thinapp for the software? Maybe that will allow for you to retain those settings that are unique per user. If that doesn't work then it sounds like maybe your use case calls for full desktops instead of linked clones.