It was probably already mentioned that in QBO's audit history there is an ID number.  It would be nice for audit purposes if this ID were searchable, and accessible in a report.  Again, maybe this was already addressed? 

A partial work-around, while not sufficiently bulletproof for auditors tracking transactions, may help many others:  Adding "Create Date" to your transaction reports will provide a pretty good uniqueID.  I don't know for sure but I suspect "Create Date is a Date-Time stamp (YYYYMMDD-HHMMSS) is set when QBO writes the transaction to their database and does not vary once the transaction is created.  Is "Create Date" unique?  Not necessarily, but if your transaction volume is not huge, it might work for you.  To be a bit more careful, try concatenating all transaction field values into one text field, including Create Date: this still might not produce a unique value, but the number of duplicates will be reduced significantly.  Hope this helps.