apps missing from itunes file

My iTunes apps file was corrupted, and I restored what I could. But now a lot of the apps are missing from iTunes.

They're on my iPhone 4S, and various other Apple devices, but every time I sync my iPhone, the sync deletes the apps from my phone that it can't find in iTunes. I've re-downloaded them onto my phone, but I can't find a way to re-download them to iTunes. So the next time I sync to add music to my iPhone that I've purchased elsewhere and imported into iTunes, all those apps get deleted again. More hours spent downloading apps back to my iPhone and placing their icons where they belong. Very frustrating. And one old app that is no longer available from iTunes, but one that I use daily, is now only on my old iPod Touch - so I can no longer sync it, without totally losing that app..

This problem first started when I tried to update to iOS 8.3 from 8.2. The update failed for some "unknown reason", and I had to restore my iPhone to the backup made just before that update. The restore dumped all my apps and all my music. When I tried to re-sync my music, it only restored about 1/3 of the songs. So I've had to re-sync again, and again, trying to get all the music back on the iPhone. And every time, it dumps most of my apps.

My questions are: Is there any way to get the old, highly valued app from my iPod Touch back into iTunes on my Windows 7 PC? And is there any way to get the missing apps back in to the iTunes file on my PC from my iPhone?