If I read your post correctly, you want to eliminate all new records if there are duplicates, not just the duplicated ones, so...
Step 1: If you want to guarantee the barcode value in your table to be unique, ensure that you force this by creating a unique index for it in table design view.
Step 2: Ensure that you have NOT disabled confirmation messages.
Step 3: Create a new Yes/No field in your table (lets call it [JustAppended]) and ensure that the values for this field are set to TRUE when first appended.
Step 4: When you run your append query and there is at least one duplicate barcode value in the records you are trying to append, you will get an error message stating that Access was unable to add some records due to key violations. This is your flag that there was some duplicates.
Step 5A: If no such prompt happens, use an update query to set the values of [JustAppended] for all records to FALSE.
Step 5B: If you get this prompt, delete all records with [JustAppended] = TRUE to restore your table to its starting point.
HTH