Can't download software from external harddrive - software already exists

So recently i started playing (the) hacker experience. Im really enjoying this game but for some reason somebody hacked me and deleted all my software. Now i've backed up some of my files but when i try to download them back to my 'software' folder it says the software already exists. Screenshots below to clarify.

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My software list

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My external HD

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The error message

Is there something i can do to use my backed-up software again?

Unfortunatly after upgrading my seeker all the way from 1.0 till 3.0 i still wasn't able to see any software that might have been hidden. I decided to format my HDD and download everything then. This turned out to work. Thanks to gatherer818 and Schism.

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