Losing apps during sync

I'm having trouble finding the answer to this question.
I keep my iTunes library on a removable hard drive, and that means my applications are there as well. If I plug my iPod in without the hard drive, iTunes wont be able to find the applications and will delete them. I can prevent this from stopping the sync, but if I want to do more than just charge it, (like add the few songs that ARE on the computer, or back up to the computer songs I purchased on the iPod), then I have to sync and I lose my apps that aren't on the computer's hard drive.
How can I prevent this? I'm sure I can move the apps to the local computer and just keep them there rather than on the removable hard drive, but is there another way?
Thanks.

Suppose I just stored the apps locally and could leave all the songs and videos on the external? If I did a sync would I still lose everything? (I manage manually, so it doesn't go through my library and update, I just lose the Apps every time unless the external is plugged in.)

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Losing apps during sync

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