Can I reinstall win98 without wiping out knoppix hdd?

[fingers99]

First when I do boot into win98, win98 doesn't recognize my linux partitions at all.

That's normal enough: Windows simply can't recognise any non M$ partitions.

As Mr Ed points out, there are a lot of ways back if Windows zaps the MBR. A dual boot system (I stopped dual booting 3 years ago and don't miss Windows at all) with a drive for each OS is safer and easier to manage, but you should be safe enough.