Question: I installed Linux on my system and everything was working fine. Today, I needed to do a fresh install of Windows 98 onto my primary partition. No problem, I have done this a hundred times before. During the install, it asked a strange question: did I want to format D: as it wasn't formatted? I answered yes and the install proceeded. Imagine my surprise after the install finished when I found out that all of my partitions (except the primary windows partition) are gone to be replaced by one single large FAT partition. This has never happened before and the only difference between this and previous occasions it that I had installed Linux. What happened?
Answer: When the Windows 98 install finds non-DOS partitions (eg. ext2 partitions used by Linux) on your hard drive, it asks if you want the Windows install to delete them. The default answer to this question is yes. When you have other operating systems on your hard drive you must answer no to this question or Windows 98 will delete everything on your hard drive that it doesn't understand. Microsoft Operating Systems are well known for trying to destroy any non-Microsoft Operating System that you might have on your hard drive. Only by reading the questions carefully during the install process and not just accepting the default answers can you protect the other systems that you already have installed.
This problem is made worse by the fact that Windows 98/SE/ME also uses a non-standard identifier for the extended partition on hard drives. Instead of using the standard x'05' in the partition table, Windows uses x'0f' which non-Microsoft operating systems may not understand. Windows 98 will work with the extended partition defined as type x'05' but the install process recognises this type as an invalid partition and will not allow the install to proceed without answering yes to delete the partition - which will wipe all of the logical partitions on your drive regardless of what partition type they are formatted as. The only way to resolve this is to change the partition type from x'05' to x'0f' before starting the install and change it back after the install is complete. The easiest way to make this change is using Ranish Partition Manager.
Unfortunately, if you answered yes to overwrite the non-DOS partitions, then you are too late to recover your other operating systems and you will now have to reinstall those as well. At least now you know what to do next time you need to reinstall windows.
This article written by Stephen Chapman, Felgall Pty Ltd.