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I am running Fedora Core 4 i386 on an AMD XP 2600+ and I want to upgrade to a new AMD64, how can i change my copy of linux over to the 64 bit ver without losing all of my files. I dont mind losing the apps but i have too much misc files to back up and reformat. Can anyone pls help me.

How do you have your hard drive partitioned? If you have separate ones var /home and data etc then just make sure you don't format those if installing. What file system type are you using?
I have successfully upgraded versions of linux by installing "over-the-top" (as you would do with windoze every now and again) and have even fixed a slackware distro that way once when I accidently recompiled half the system for the wrong CPU architecture! I had forgotten I had switched the hard drive into an AMD based system and recompiled stuff for P4 = dead system. Reinstalled over the top without formatting any partitions and I was back to my cutomised desktop in no time.
I don't have any experience with AMD64s, best advise I can give would be to make sure you have working backups on either CD/DVD or a separate hard drive just in case....

all of my files are on one big partition. So is it OK to install it over the top of the old copy of linux.

Yes, and make sure to run Yast and install the newest updates. Also, make sure your hardware is supported and all your drivers, in teh 64 bit edition.
Always check the manual first, Google helps too.

One other thing. If you use Plesk on Fedora ore four, you may need to reimage.
Always check the manual first, Google helps too.

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