After operating system upgrade my iTunes doesn't have my Apps

I updated my MacBook Pro to the new operating system today.  Unfortunately the update crashed my iphone and i had to restore it to the original settings and then restore it from my latest back up (which fortunately i backed it up today).  However, I only have about 10% of my apps on my phone.  I then went to iTunes to try to restore my apps from there but I can't find the list of all my previously purchased/downloaded apps.   Please help!

I've been fooling around and discovered a couple of problems.  I couldn't understand why apps I KNEW that i paid for and were on my phone were now showing up as a charge.  Turns out I have overlapping problems at play here.  I purchased a MacBook Pro a couple of months ago and a friend set it up for me.  Turns out that he didn't make my MacBook "authorized" for my iTunes account.   I did that and then the apps changed to show "downloaded" so I no longer had to pay to download it again.  I thought I had solved my problem.  But the apps still weren't showing up as a list for me to sync.  I downloaded a couple again, hoping that it would help me find where they were going, and it did go to the screen that showed what had been downloaded and the pages from my phone.  I tried to sync and received a warning.  Apparently my apps are all connected to my iTunes library from my old laptop (which has been reformated and given to my Mom so thats not a solution).  It says that if i sync now, i will forever lose all the apps i have in that other library.   
Any ideas how to fix this?    I could start from scratch... but i hope I don't have to do that.

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