What is the most efficient way to clear "bad" transactions from TM Module?

Summary:

We need to determine the most efficient way to clear "bad" Transaction data in the Transaction Matching module for reloading good data so that we don't have to manually delete transactions from 100s of reconciliations.

Content (required):

We use Transaction Matching to match a high volume of transactions for 100s of reconciliations. There is a chance the admin could accidentally load a "bad" transaction data file into the system, causing our matching recs to populate with bad data. We understand we can manually delete transactions en mass from each rec. However, this could mean doing this process for 100s of recs, which is very time consuming. We need to delete the "bad" transactions before reloading the "good" transaction data file. My understanding is that the "good" transactions will not override the transactions loaded in the previous file.