I should have posted that we were able to finally resolve this issue. I spent probably close to 40 hours on the phone with various support people, data recovery, etc. No one at Quickbooks seemed to know what or why this was occurring. They all defaulted to the generic "update the file", "send it in to Data Services", etc.

The issue, for us, was related to the Melio bill pay integration with Quickbooks. I had reset the users Intuit accounts and to reset/create a new Melio bill pay account. Once that was done, everything returned to normal. I don't know how or why the synching got thrown off. We use RightNetworks as our cloud provider but do not know if that has anything to do with it.