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It sounds like Win 2000 was installed after the Linux install. In this case the MS OS would over write the previous Linux Boot loader. If you made the emergency boot disk during the Linux install, you have options, if not ...... You're looking at a re-install. I have heard rumours that the Linux Boot Loader doesn't co-exist well with Win 2000. I think the claim was the opposite of what you have, meaning the win 2000 would not boot. I don't work with win 2000 personally. Many people prefer to use other bootloaders for win 2000 installs with linux. I have no experience with these.
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