Why did syncing with iTunes delete one of my photos folders?
Suggestion 1 :
I think you would be a new user to the iPod/iPhone/OS X/iTunes family. 
If your afraid or don't understand what is happening during synchronization using iTunes, I suggest you to use a utility called iPhoneExplorer.

Just Explorer the iPhone/iPod/iPad like a file system. You would get your images under Root/User/Media/DCIM/ directory. images are grouped in directories like 100APPLE, 101APPLE and so on. Just explore and copy it.

Suggestion 2:
Synchronization - means A single machine and an iPod synchronization. Not multiple machines and an iPod. If you synchronizes from other machine it will erase all of your old data. According to me, you had the problem just because you might have synchronized from other machines iTunes.