You already mentioned MSC5N in the sucject, does it not do a mass change for deletion indicator?
In any case you can use LSMW, for deletion and for loading the batches with your desired number.
But not sure if you are missing something in the scope: the stock.
If your batches have stock, then you need to issue the stock and load it again to the new batches.
How is your material labeled? in the desired right way or equal to the number in the SAP system?
And not to forget, your original movements still have the wrong batch numbers, and they will stay until you archive movements, so not really sure how worth the effort of changing the number really is. You will find the wrong numbers in statistics for a long time too.
Later you can archive the batches with SARA and object MM_SPSTOCK, but batches are a kind of master data, hence the transactional data, purchase orders, deliveries, production orders, short wherever those batches are used has to be archived prior to the batch.