Most cheap generic drugs are imported by the containerload, so simply create an arbitrary "batch" from each instance of importation. If the manufacturer is decent and has its own batch number, then the label could read
"Manufacturer batch: XXXX FDA Import of Record batch: YYYY."
Drugs that are imported in more specialized ways -- e.g. by small-volume refrigerated air freight -- are, as a general rule, far more expensive and batches are correspondingly smaller. The above paradigm would still work, where each importation instance is, for the FDA's purposes, a batch.
Testing fees, which shouldn't amount to more than a few thousand bucks per import, can be the responsibility of the importer -- so as to dissuade importers from receiving small batch after small batch.