This could potentially be an issue of Target Chaining. 

The most common ways of identifying this issue:

• Open the Unpaid Bills report and look for old bills that are unpaid but should be paid
• Open the Vendors > Pay Bills screen and check for unpaid bills
• In the Chart of Accounts, check if the Accounts Payable account is extremely negative
• Open the Profit & Loss report and check for large balances in Uncategorized Income or Expense
• Open the Vendor Balance Detail and look for negative balances and/or bills showing under No Name
  
  

It is a current limitation in QuickBooks, not a bug. QuickBooks was designed for Small to Mid sized Businesses and this issue only occurs after the file has reached 2 GB or has over a million targets.

Make sure the Cache has been set correctly. 

If possible, restore a backup from BEFORE this happened, typically you should have a backup created right before the rebuild.

If you do, perform the following on your system where Quickbooks is Installed. This should prevent the target chaining issue from happening.

Browse to the respective QBW.INI file stored in

ProgramData: C:\ProgramData\Intuit\QuickBooks Version\

Add the following:
[DBSERVEROPTIONS]
InitialCache=4096M
MaxCache=0

Save the Ini File. 
Be sure Quickbooks is closed out completely as well. 
Restart Quickbooks.

You should be able to see what your current Cache is by clicking F2 and pulling up the Product Information window. Your current Cache will be in the bottom left hand corner. You want this to say "Unlimited".