To manually reconcile a credit card re-imbursement in Xero, you will need to utilise the "Transfer Money" feature in Xero.
1) Click the reconcile button for the relevant bank feed
2) Find the credit card re-imbursement payment and click "Match"
3) Click on New Transaction > Transfer Money
4) Enter the amount that was transferred (excluding fees) > Choose the account the funds were transferred to > click on Transfer
5) Xero will then advise the amounts do not match. You will need to click on Adjustments > Bank fee to account for the processing fees paid > click on Reconcile