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Buy nowHi, @T_Hor. Thanks for joining the thread. Let me help you fix this.
There may be damaged links between transactions or the transactions themselves that's why it does not appear in the Payment section. I recommend that you run the verify and rebuild data tool. This enables us to see any data issue within your company file.
To run the Verify Data utility:
Here’s how to run the Rebuild utility:
It may take a few minutes for the process to start depending on the file size of your company. When the rebuild tool is complete, run the Verify tool again to check the remaining data damage. Otherwise, if you received the message stated above, then you're good to go.
You can also visit this article to learn more about depositing payments: Record and make bank deposits in QuickBooks Desktop.
Let me know how it goes on your end. I'll be around to assist. Stay safe and have a great day!