Record net negative Stripe deposit when refunds exceed payments?

We have a low volume Shopify store using the Stripe payment gateway. We process store orders (monthly) in QB Desktop as follows:

1. create invoice(s)
2. receive payments on “Visa” leaving the box to process payments unchecked
3. record deposit, adding a line to reduce deposit amount by Stripe Fees (an expense account)

This month, a paid but unshipped large order from several months ago was refunded from within Shopify/Stripe, and another unrelated small order was received. For example:

• REFUND: -100.00
• REFUND ADJUSTMENT: 3.00
• NEW ORDER: 50.00
• NEW FEE: -1.00
• NET RESULT: -48.00 (pulled from checking acct)

We entered the new order invoice as normal, then created a Credit Memo for the refunded order, and chose to refund to back to “Visa”, and left the process payments box unchecked. However this makes the total to deposit a negative, which cannot be saved in QB.

Question 1 – should we have wrote a check instead, for $100 minus the $3 adjustment, then entered a deposit for the new order only?

Question 2 – if writing a check for refund, is it appropriate to use the Stripe Fees account, for $97 out to customer?

Question 3 – unsure how to remove the unprocessed Visa refund. Will voiding the CM clear it out?

Thanks!