Re: How to correct undeposited funds?
Change both systems. Make one Other Current asset account and use this for Funds in Transit.
What you have right now is a great way to corrupt a QB Desktop file, because you never post Manually to or from UF or using JE for UF. It is a self-managing and self-reconciling account.
Change everything to stop using UF. That is a type of asset with Specific internal functionality. Use your own Bank type or Other Current Asset type. If the funds in reality already went to Checking, just change the use of UF to Checking. You don't need a holding account awaiting settlement, apparently.