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Changed drive from NTFS to FAT32, DOS and win-98 doesn't boot

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I had a spare 400 gb sata drive that was pulled from an old XP machine that I wanted to temporarily slave to my win-98 machine (intel 845-based motherboard with 2-port SATA controller add-on PCI board). I disconnected one of the two SATA drives connected to the PCI card and connected the 400 gb drive in its place. Windows 98 booted fine, but (as expected) did not see the 400 gb drive.

I then booted into DOS and ran free fdisk 1.2.1 where I deleted the single NTFS partition on the 400 gb drive and then created a single FAT32 partition (I did not reboot between those 2 actions). I then rebooted, but the system would not boot.

I tried pressing f8 during startup, but that menu never came up. The bios was set to boot floppy first, then drive-0 (which is an IDE connected to Master primary). I disconnected the 400 gb drive and was able to boot normally.

I set the bios to only boot from floppy, and a floppy formatted with win-98 dos (format a: /s /u) with no config.sys or autoexec.bat booted normally. But the floppy won't boot with the 400 gb drive connected to the system. Even if that's the only drive (no other IDE or sata drives) the floppy shows disk activity for about 10 seconds then stops.

I'm going to take the drive and slave it to another (XP) system and mess with it until I'm able to connect it back to the win-98 system, but I was wondering what sort of state the partition table must be in for DOS and win-98 to freeze up during boot when the drive is present. ?

I've connected many IDE and sata hard drives to various win-98 systems in the past and have never encountered a situation where just physically connecting a drive to the system prevented full booting into win-98 - or even DOS.

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I have. I created such situations in some of my experiments. Slave it to XP and remove the Partition. Refresh the MBR as well. Then you should be able to access it from DOS.
Use the DOS FDISK to recreate the Partition.

Connecting a SATA Drive can disable Windows 98 if it does not have the proper SATA support. This would not affect DOS though.
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