Do you have ledger data? If so, then printing the report will never clear the file. You have the option of consolidating but not clearing.

The correct procedure here would be to open the ledger program (Adagio or Accpac Plus) and retrieve the sub-ledger batches for AR, TB or whichever appropriate applications there are.

If you do not have ledger data, then printing the GL Transactions report will give you a second message 'do you want to clear the file' after the consolidation question. Note you have to print the report to paper or a file (not previewing) to get the clearing message.