I'm here to ensure your deposit post on your project in QuickBooks Online (QBO).
It's possible that when creating a deposit, the project name was not associated. To verify, we can search the transaction and see where it goes.
Here's how:
On your QBO account, click the Magnifying glass at the top.
Click on the Advanced Search link at the bottom.
In the Search field, select Deposits.
Set the other filters.
Click Search.
From there, locate the deposit and ensure that the name under the Contact column was the project. If not, then that's why it's not showing on your Project. To solve this, I recommend correcting the deposit.
Once done, go back to the projects and check if the deposit is now showing.