edit-If it's some kind of game you will lose all the stats, though.
I'm struggling with this issue at the moment and unknowingly wiped out all the data in my apps, which was quite a shocker given the time I'd invested in these things. I'd like to think there's a way to work around this! What if instead you do this: Once you've moved your itl database file to the external drive (or new drive, whichever), instead of manually copying over and readding the mobile apps folder you instead resync your phone?
Theoretically, the app on your phone is the most up to date version in terms of the content saved within the app, so when you plug in it won't the app copy back over to iTunes and maintain your goods? Or will iTunes still be looking at the app and backing up to the old location?
One more question on the subject (Katrina, you seem like the go to expert for external drive itl management!): I'm attempting to use my external iTunes library across both Mac and Windows. My music library has been living on my Mac for awhile, and that's where I'm trying to move everything from. I started off by redirecting my music folder to the external drive (which is in Fat32 format) and then running the consolidation process to copy everything over. After that, I manually copied over the iTunes library files and then tested it out with an Option-button start to choose the library on the external. Everything seemed fine, until I plugged the drive into Windows, where the following things occurred:
1) When running a Shift-button start to choose a library, I couldn't originally find the library file on the external because Windows was looking for a file with the extension itl, which the Mac had not included. I manually renamed the file, though, and it loaded up just fine.
2) Things looked okay at first, until I started browsing through my library and discovered that a number of songs had exclamation points stating they could not be found. At first it seemed very random and when I checked the actual folders in Windows Explorer, the files were there. It took a few moments, but I finally noticed a common trend: They were all long song names, and thus long file names. As it turns out, at some point in the process, long file names were truncated, but the iTunes Library file is still pointing at the full filename. I haven't had a chance to go back and try the process again to see if I can figure out which step led to the truncation, but I suspect I'm not the only one this has happened to.
Any ideas? Anyone? Bueller?