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I am going to replace a hard drive that has 204 reallocated sectors, but if I use Clonezilla to duplicate my files, settings, and programs to the new hard drive, will these sectors affect my new drive in any way?

I am looking for a more detailed answer for #3 of my previous question (already answered), with explanations as to why the sectors should or shouldn't affect the new drive.

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The reallocated sectors are drive specific and do not mirage to a new drive. It is simply the drive pointing out to itself, "Hey, I can write data every where but here, here and here" (204 "heres" in your drives case). When the disk identified that the sector is troubled, it moves any data in that sector to a safe place and remaps it's activity to work around that sector. This is why when the reallocated sector count rises, disk performance can show a noticed degradation.

If all your files, settings and programs are working fine now, they will be fine after the cloning.

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thank you for the confirmation! – Ethan Lee Aug 11 '12 at 22:06

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