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The current working directors is, e.g. /media/username/ExtHDD/.
When disconnecting and re-connecting that HDD, commands such as ls do not work properly anymore.

$ -????????? ? ?    ?             ?            ? Filename.txt

Why do I have to use cd / ; cd /media/username/ExtHDD/ before the commands work again?

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When you eject a drive, all information about that drive and any processes attached to it, is discarded from the working memory of the operating system.

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