Unfortunately the Parallel Port software is notoriously prone to crashing. There isn’t much you can do to prevent it from happening but you can be extra careful when restoring saves to the card. A software crash when sending a save across can at worst fill your card with corrupt data needing a format to remove or corrupt the existing saves on the card.
So before sending any save across be sure to backup the saves on the card, it only takes a few minutes and saves a lot of heartache.
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EMS Memory Adapter FAQ