Problem syncing iphone with old computer with a new hard drive

So my macbook's hard drive died and I had it replaced. I used an external hard drive to transfer my old library back onto the new hard drive.

When I try and sync my iphone, itunes prompts with a message saying there are apps that are on my iphone that aren't on the computer and would I like to transfer these to the computer.

After I click on yes, it tells me this computer isn't authorised for this account. Then it gives a new message saying I have already authorised this computer. After clicking ok, it then gives me the first message again and wants me to authorise the computer..... an endless loop.

I have tried restarting both items, deauthorising and reauthorising all to no avail. Any ideas?