well first off windows 2k/xp cannot be installed freshly on a 1 GB drive. Secondly just because linux was installed on this drive doesnt mean windows can. Also, your hardware might not support boot from this type of drive. In BIOS is it showing up as an IDE drive ???
What file system are you planning on using 2k with ? I suggest you try using fat32. Format the drive using a boot disk using the /s switch, (example: Format c: /s) This will put the system files on the target drive. Once the machine reboots w/o the boot disks in any drive you've proven that your machine can indeed boot from the micro drive, prodived you get the command prompt w/o errors.
If all that works out, install windows on a normal HDD. Make sure its under 1GB final sized and no file compression is turned on. From here I suggest use xcopy (search for the proper switches, there are a bunch that you'll need) or Norton Ghost (if your able to get a copy) Although I dont think ghost will copy an OS onto a 1 GB drive...



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