IPad's apps not showing in iTunes app management

Hey!
We have iPad Air and now a brand new Macbook Air. After getting everything back from old Macbook Pro to MB Air using Time Machine I started to tweak with iPad again.
It finds the iPad just fine, sync seems to work, but in Apps tab I can't see any of the apps installed on iPad in the left column. I can't now move files between the laptop and iPad's VLC Player because of this. All the softwares is now up to date, but before the old laptop broke, it used older osx and possibly iTunes as well than now. Maybe sudden update to these have caused some kind of glitch and prevents me from seeing the apps using Macbook..? Any ideas?

Well, I don't really use iTunes that much, so there weren't any content in the library to recover. I have just installed a few apps straight to iPad using appstore on it. I use iTunes just to move some movie files to VLC.
So, at the beginning, I had
- Older MBP running Mountain Lion and possibly older version of iTunes. Also had iPad with few apps including VLC, installed on it straight from AppStore. Could access VLC in File Sharing menu via iTunes.
Then the laptop got broken and now
- I got Macbook Air with latest osx and itunes. Files and settings recovered from Time Machine. Everything seems to be in place and iPad gets recognized by iTunes
- When plugging iPad in, I can see apps installed on it for a while during sync (if I select Apps tab in iTunes as soon as I plug it in). The icons are grey and after sync is complete, they disappear from the list completely and I'm left with correct screenshots of iPad on right side, but nothing in the list to actually access the apps.
Edit: and to answer the question, the apps are still on iPad and running just fine. The access just isn't working for some reason

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