Thanks for reaching back out! 

My mistake. Previously you were able to process credit card payments through QuickBooks Desktop, however this changed in October of 2018. Take a look at this helpful article that goes through changes to QuickBooks Desktop Merchant Services as of October 1st 2018. 

In regards to removing the payment information for your customers, this will have to be done manually. I know you've got a lot of customers and deleting the payment information for each person individually can take time. You may decide to leave their payment information in the system, since it's password protected. However, I can certainly appreciate not wanting to have it on file.

I appreciate your feedback about the process to remove the credit card information from the system. I'll certainly be passing this along to my team.