The migration tool that Mailchimp built will not work with the Abandoned Cart Email (Series). As a result, you will need to recreate these after installing ShopSync to get them sending again.
Use Mailchimp's migration tool
After ShopSync is installed, you'll want to follow this how-to guide to migrate your automations. In there, you'll see a steps that should help you get things restarted. As noted above, the abandoned cart series will not migrate at this time. This is nothing that ShopSync has control over, it's an internal limitation confirmed by Mailchimp's technical team.
If for any reason they don't restart, you'll want to reach out to Mailchimp's support team for further assistance.