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originally posted by: Goteborg
Are you the owner of the encrypted files or do they belong to someone else? If you're the owner of the files you have a couple of options. You can decrypt the folder before you copy it to USB when you're on your Windows machine, if that's not an option you can retrieve your private key when you're on your Windows machine and then use that to decrypt in Linux (probably).
If this is for personal use or if your employer doesn't have a problem with third party software being used then I agree with the other poster, just download a program that will decrypt it for you.
originally posted by: Attentionwandered
Format the thumb drive to Fat 32, that should work in linux and windows. Then, encrypt the files on an individual basis using .rar or .zip with 7-zip or whatever software. That way, if one pass code is compromised your other files may still be safe.