Can I still process an incomplete order of the customer who was deleted by GDPR? Will all related order data of this customer be deleted also?

Yes, you can still process all incomplete orders of this customer. The customer's order data will not be deleted.
The GDPR module helps remove the existing customers' information which means that after deleting, if they place an order again on your store, they are perceived as a first-time buyer with no data remembered.
Deleting customers' data doesn't affect the order data.
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