Hello again, Risho,
Thanks for all of the details about what you've done up to this point to record the prepayment in QuickBooks Desktop. I know this process has a few steps to take and it sounds like you may be familiar with them considering what you've outlined here. I want to make sure you've got the right steps to get this logged correctly.
I recommend starting with the Record supplier prepayments or deposits for prepaid parts or services article, which walks you through how to create the cheque so that it later shows up as a credit for you to apply against the bill. The important part of the process is to make sure you're choosing the Accounts Payable account for the amount that you need as the prepayment for the bill.
With that in mind, the thing to check on is how you entered the cheque into the system. I see you mentioned that you've chosen the Accounts Payable, but it doesn't hurt to double check it. If needed, you may be able to simply edit the category to Accounts Payable if that's what you need to do, but it may also mean undoing the reconciliation to complete the corrections and then reconcile again afterward. Undoing a reconciliation is as simple as clicking the Undo Last Reconciliation button when you go to the Banking menu and choose Reconcile.
As for locating that cheque, you can look under the vendor profile in the Vendor Centre or using the Write Cheques feature and hitting the back button to find it.
If everything looks to be as it should, I recommend checking for data damage to your company file. Don't worry, I've got an article that walks you through this process so you can know what to expect: Fix data damage on your QuickBooks Desktop company file
Give those things a shot to start and let me know how it goes. I want to make sure you're good to go with this.
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