Other general items to check when having QuickBooks Integration Issues:
Account is marked as Active in both e-manage & QuickBooks. Check in QuickBooks by navigating to Lists → Chart of Accounts → Right Click on Account → Edit Account → Ensure “Account is Inactive” is not checked. In e-manage navigate to Finance > View / Configure QB Chart of Accounts → Account is marked as “Use in e-manage” and the “Receivable” and/or “Payable” boxes are ticked.
Check if the Customer or Vendor is setup in QuickBooks and that the Company ID matches. If you edit the Company Record in QuickBooks you run the risk of breaking the connection between e-manage and QB for that Company. You can check the “Company ID” in e-manage by navigating to Today → Companies → Locate the Company Record → Check the Company ID field. This should be the “Account Number” on the Company Record in QuickBooks.