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Confused restoring boot partition

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I was having problems booting, and Windows did its own system restore to an earlier date. So now I have a bootable system, but allot of things are broken (things trying to run files that have since been deleted, uninstalled programs showing up in control panel, etc)

I have a very recent backup from Acronis, and I was going to restore it from the Acronis boot disk, but there was somthing that makes me afraid to do so. When I go through the restore wizard, I get to the screen that lets me check boxes to restore 3 items. (System Reserved, Boot Sector, and Main/Bootable Partition) In the following steps, it looks like it is going to restore the System Reserved to a "C" partition and the Main/Bootable Partition to a different "D" partition. My current bootable partition is "C". I am afraid proceeding with the restore at this point would really mess things up. Am I misinterpreting what I am reading and what Acronis is really going to do?

Thanks,

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If your disk had only the system reserved and the C:\System partition, then check the box that is just left of the disk name. The three boxes below (one for each partition/component) will be checked automatically. Then proceed to restore. Restore also the disk signature (this option appears on one of the last screens)

Do the restore from the recovery disk.

To answer your question nevertheless: the partitions letters you see when you do a restore are artefacts of the UI of ATI, and are generally different from the ones you see in Windows. Just ignore this. When you restore a single partition, what is important is that you restore to the right one, despite the difference in letters. No need to fix this by trying to change the drive letter (an option during restore). When you restore the whole disk, it doesn't matter at all.