I have a problem adding my library to a new iTunes installation.

Some background:
Originality the library was on a desktop PC I used iTunes to move the library to an external hard drive as I had a laptop. That worked fine and I was able to uses the ext HD as a network drive an point to it from iTunes.
I had a problem with the laptop and had to reinstall windows and was unable to backup the library (which was fine as all the music was installed on the Ext HD) however after installing iTunes I cannot import the library, I was able to add all of the music, however when I connected my iPod it said that it was not a registered computer and would have to re-sync, this would be fine except I have quite a few Apps that I pad for and downloaded on the iPod and by re-syncing I will lose these, is there any way to get iTunes to import this library of get my Apps in to this library?
Thanks.

There should be an option to sync purchases from the iPod to iTunes.
See this -> Copying iTunes Store purchases from your iPod or iPhone to a computer
i cannot re-download them for free
Yes you can.
Click on Purchase and iTunes will tell you that you jhave already purchased then and ask if you want to redownload them (for free).

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