Can I get rid of my faulty disk permissions by upgrading to Lion?

I just replaced my hard drive for my MacBook. I took it to an Apple retail store, and they installed Snow Leopard. I restored the system to what I had on the previous hard drive (which had faulty disk permissions). I was told that the permissions were in error because of the failing hard drive. I even asked if I restored from my old hard drive if those faulty permissions would pop up. They said no, and that I could even uncheck the settings box on the transfer when I first started the computer. So I ran disk utility, and wa-la. Faulty disk permissions. If I upgrade to Lion, will it overwrite the system? Will my faulty disk permissions leave me in peace?

Check apple's list of permission errors you can safely ingore at  http://support.apple.com/kb/ts1448
I had a few permission errors that Disk Utility always warned me 'could not be repaired" that had me thinking I had a serious problem - -turns out it wasn't such a big deal

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