John,
By design, Globus sharing permissions are always an overlay over the local permissions. If the local user no longer has access to the data, then anyone with whom the local user has shared data can no longer access data either. In other words, there is no way for a sharee to retain access to data if the share owner can no longer access the data. Unfortunately, that can put people who rely on access to data via shares in a difficult position if the person that shared the data no longer has the right to access the data. In some cases, creating a new share with the same name and permissions as the old share is an adequate workaround. If you are interested in developing scripts that will create new shares with the same meta data and permissions, you can
email sup...@globus.org for guidance.
I'm sorry I can't give you a better solution for your current situation. But for the future, as you suggested, a service account is a good option for ownership of shares or guest collections that should be owned by an organization rather than an individual. One option is to register an app at
https://developers.globus.org/, and then map the app to the local account that owns the data (detailed mapping instructions are here
https://docs.globus.org/globus-connect-server/v5.4/identity-mapping-guide/). The app credentials can then be used to create shares or guest collections using the Globus CLI.