Your question seems very familiar and I think that I answered a question very similar to this.
I don't know why it would disappear from iTunes - because that is a function of the iTunes app on the computer.
Did you try reinstalling iTunes? Or in the interim, have you tried just dragging the files into the file sharing window?
Connect the iPad to the Computer and launch iTunes.
Click on the iPad name on the left side under devices.
Click on the Apps Tab on the right.
Click on the app that you want to share with in the file sharing window of the apps tab
Drag the file from the desktop into the file sharing window on the right.