I also have this problem and it makes no sense to me whatsoever.  I screwed up all of 2018 because AR and undeposited funds were totally off causing huge totals in each account even though I reconciled.  ( how can you reconcile if QB has your deposit sitting in some AR account???)  When I import a deposit, why doesn't AR just recognize this and reduce the balance?  that makes sense.  I am just starting to put transactions into 2019 and I don't want this happening again.   I also have to delete expenses that were charged to a job because those expenses are included in the invoices making more transactions in AR and therefore making AR even bigger.  These expenses are included in our invoice.  The CPA did an enormous journal to take the unwanted charges out of AR and begin 2019 with a zero balance.  Now I need some step by step instructions on how I am going to keep AR and undeposited funds from becoming enormous again.  Does anyone have those steps?  No one seems to know how professionals invoice and all I see are instructions for inventory type businesses.  so here is the deal.  I prepare an invoice that includes the expenses that were on T-sheets.  what are the steps I have to take to keep AR and undeposited funds correct?  Just delete the fees before reconciling?  If I do that, how are these expenses charged to their jobs?