Several months ago I had a $5K client deposit disappear as well. The client showed me his CC receipts so he most definitely paid me. The money never showed up in my QBO checking account. After weeks of reaching out to QB one gentleman explained to me that there was a Green Dot software issue (?). He said the best thing to do is to make another account (maybe a personal or another business account) my primary bank rather than QB bank. The change can be made easily within the QB app. The money appeared almost instantaneously. I stopped using QBO as my primary bank which sucks because I liked the convenience of it.

I recently tried to transfer a small test amount of money from my personal bank to QB  bank. It still doesn't work. The money did NOT make it to QB bank.