Never ran into this, but on first pass, I know that the Integration for Sync only allows one credential, so if you are looking to sync to one instance - that is where the control is for what gets sync. The documentation seems to imply that you can setup multiple integrations to different instances, so that is what you should try and see if that allow for both instances to sync to Genesys Cloud. Rember, this is a one-way sync (kind of an oxymoron if you ask me), but it will only take information FROM Salesforce and create contact in Genesys Cloud. It will not take any contacts in Genesys Cloud that were not synced and update Salesforce.
Didn't really give you a good answer, but at least it gives you options. In my opinion, it should not affect any contacts you created or uploaded in Genesys Cloud directly.
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Robert Wakefield-Carl
Avtex Solutions, LLC
Contact Center Innovation Architect
robertwc@avtex.comhttps://www.Avtex.comhttps://RobertWC.Blogspot.com------------------------------