IPod & iTunes not sync right :(

I used to have my iTunes installed on my main drive (I have a slave drive)but when my main drive was almost full of songs, I asked for an external drive for xmas and got one. So I uninstalled iTunes from my main drive and installed it on my external drive where I've transferred ALL my mp3s. Now since then, I've updated my iTunes and gone ahead and plugged in my iPod but even though the iPod says "do not disconnect" my iTunes on the external drive doesn't seem to be updating the iPod. I go under "File - Update iPod" and the option is greyed out. I listened to my iPod and noticed that songs I had originally deleted on iTunes were still on my iPod, is there any way to resolve this issue?
I'm wondering if the iPod is still reading information from my main drive, though the entire iTunes folder including all mp3s have been deleted from it.

fixed!

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