Reverse cloning
I recently attemped to clone my boot disk to my secondary HD and found that the process has run backwards and the boot drive is now a prevoius clone that will only boot windows in safe mode with all recent data lost. I felf I took extraordinaty care to prevent this carefully indentifying disk 1 and 2 by name. Fortnuately I have all data backed up but the thought of reinstalling Windows XP from a 2002 disk is more than I can stand. Any help would be appreciated.

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Do you have any TrueImage backups of your C partition--even if they are old?
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Only the one that got copied back onto my boot disk.. Unfortunately this boots only in safe mode.
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I'm not criticizing you but there is a point to be made here about backups for everybody in general.
Never only have one backup of your system even if it is a current one. Something can go wrong with it and then you have zero backups. This happened to me because of a sector on the backup drive going bad but I had another image not too far out of date.
If your favorite backup method is to make a clone of the disk then you should get at least 2 target disks to make clones with. This is where imaging shines over cloning, you can keep as many versions of image backups as you wish within the capacity of the backup media and you can backup selected partitions rather than having to do the entire physical disk.
There are pitfalls/issues with every method and in the method above, storing all your images on 1 drive is a single-point of failure. To reduce this I copy selected (not every) images to a USB drive at suitable intervals (principle backup storage is a second internal HD).
Your data files are typically the most important thing to have a good backup for - reinstalling Windows and Apps is just a pain but it can be done. This leads me into the second issue that based on reading this and other forums for a long time is plain old housekeeping. Carefully store in an orderly fashion all your application CDs and downloaded programs you use. With even more care, store their serial numbers both with them and also consider creating a file where you record everyone of them. There have been lots of posts where the real issue for panic was lost downloads and serial numbers besides having them stored properly does make reinstallation so much easier and quicker.
Keep copies in a special email folder of all emails pertianing to the purchase and serial numbers of a downloaded product. This forms an additional level of backup.
I now alight from my soapbox.
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David,
If you can get into Safe Mode, have you tried the menu option "Last known configuration" or the windows system restore points.
Another possibility might be to run the Windows System File Checker utility which is SFC from from the prompt. Typing that into the prompt will list the options possible.
Some links:
How to fix a computer which won't start
http://www.microsoft.com/windowsxp/using/setup/support/nostart.mspx
http://www.bleepingcomputer.com/forums/topic43051.html
Microsoft SFC
http://support.microsoft.com/kb/185836
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