Overview: If at all possible, it's best to AVOID deleting transactions in one application or the other. A preferred method is to add a reversing entry. For example, add a vendor credit to offset a no-longer valid bill.
If a transaction is deleted from one of the applications, the SPRCHRGR Sync Tool will not notice this and it will not remove a transaction from the other application. As a rule, transactions only sync once. The Tool is not designed to run continual data checks.
Best practices suggest reconciling Accounts Payable between the software applications on a regular basis and reconciling cash to the bank statement each month. This is where you would discover discrepancies caused by deleted transactions.
If you find a vendor bill, bill payment, or vendor credit transaction was accidentally deleted from BQE Core, the best practice is to use the manual import option in the SPRCHRGR Sync Tool. Pick that specific transaction that has to sync back over and run the sync. As a rule, you can also open any transaction for editing and then simply save; that will flag the transactions as having been recently updated which will cause the regular sync to pick it up. Once the sync or import is complete, confirm the transaction is in BQE Core.
If you find a vendor bill, bill payment, or vendor credit transaction was intentionally deleted from BQE Core, investigate the reason and consider implementing a process for recording a reversing entry with a full description instead of deleting transactions. If the deletion is appropriate, delete the transaction from Bill.com as well. Syncing will never delete a transaction. Consider reconciling Accounts Payable and Cash again after any deletions.
SPRCHRGR recommends creating and documenting an internal Standard Operating Procedure for handling voided Accounts Payable transactions consistently and completely.