Delete the linux partitions with fdisk and recreate them.
Upgrading Your linux Distribution mini-HOWTO
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12. Delete the linux partitions with fdisk and recreate them.

The installation guide will explain how to set about doing this, which will destroy the old system. From now on you're dependent on the quality of the backups you made in the earlier steps! You have been warned!

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Boot from the new installation's boot and root floppies. Run the new linux installation.