Since you posted it thru payables and not receivables then it will still show up in the debit column of bank rec.  I believe the Deposit slip is only for receivables but there is no reason why you cannot create a manual deposit slip to put this particular refund chq into the bank account.

Hi Eric,

Since you have already done the refund by doing a negative purchase invoice or negative payment, money has already been put back to your account.  If you deposit it again, you will debit your bank account 2 times.  

For cheques to be shown up in the deposit slip window for selection, it has to be done in the receivable module.  

If you really want to have that refund cheque shown up for selection, you will have to create a one-time sales invoice using cheque as the payment method.  It will then debit your cheque or cash ready to be deposited account and credit another account of your choice.  By making this entry, you will be able to select the cheque in the deposit slip window.  

After doing the deposit slip, you will need to make a general journal entry to reverse the one time sales invoice, so double debit to your bank account will be avoided (credit the bank account and debit the account of your choice used in the one-time sales invoice)

Hope this helps