Can I change my existing recurring invoice subscriptions to auto-charging subscriptions?

Due to technical limitations, you can't just turn on the auto-charging functionality for your existing recurring invoice subscriptions. Recurring invoice subscriptions don't have the credit card info and authorization linked to them. This is why you can't just turn on the auto-charging functionality for these subscriptions. 
If your customers want to have an auto-charging subscription, they will have to place a new auto-charging subscription order in your shop. 

The other workaround here is to create a quick checkout link in Seal Subscriptions > Subscription rules > Quick Checkout Wizard and then send this link to the customer, so they can complete the initial subscription order and start a new auto-charging subscription.