Hello Leo,

Subscription will marked as hold when refund done or you can added is manually from backend. Once subscription marked as hold , no further action will be taken on that subscription, means you can't activate that subscription again.

If refund done on that subscription then no issue in deleting this subscription. But if user paid for the subscription and you manually hold that subscription, then in that user can compain why his subscription is in hold status or removed. User need to purchase this subscription again but if he has already paid you marked as hold then you need to create subscription for that user again from backend.
Refer below mentioned document for creating subscription from backend.
https://stackideas.com/docs/payplans/administrators/administration/create-subscription

Update me if you have any query.