How to move Mobile Applications folder while sharing an Itunes library

For reasons that would be long and hard to explain, I decided some times ago to open a second user on my Book Pro dedicated to my music collection. The collection required to be stored on an external HDD, so the second user's Itunes folder links to a folder where all music is stored, and I put it with all library files (xml etc) in the Shared folder. Now I have decided to let the primary and mostly used user to share the same music of the secondary one. I easily succeeded in doing this, just simply opening the primary ITunes and ask it to link to the Itunes folder under the Shared folder. I have got my entire library also from the primary user, with covers and so on.
The trouble is that I use to manage an Iphone with the primary ITunes, and since I have not moved the Mobile Application folder (and what more?) into the shared ITunes folder, I cannot see anymore all data and applications into my IPhone section under ITunes, and I do not want to run experiments, doing a sync and just running the risk to lose all. How can I share the same ITunes library between two users, but to allow one of those still to see the IPhone data that was originally managed only from her ITunes, that now addresses to the ITunes folder under Shared folder that addresses to a HDD?.....