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recovering cygwin settings after a Win98 anomaly

Hello all

This sounds like it should be a FAQ question but I couldn't see it there. 
Sorry in advance if this is tedious.

A few days ago my OS (Win98) inexplicably reverted to a much earlier
registry version, resetting all program preferences and file associations
etc. Big headache--and recent registry restore files were all wiped at the
same time, so I can't fix everything in one fell swoop. The registry was
reset to a time (4 years ago!) when I didn't have cygwin installed, which
I presume is the cause of the present problem I am having. Cygwin boots
into the wrong folder, and won't recognise commands apart from pwd and cd
(as far as I've checked--no ls etc). If I cd to my home directory and try
to run one of my executables there, I am told that cywin1.dll doesn't
exist, though windows sees it fine (in c:\cygwin\bin).

Everything was running v smoothly before the anomaly. Is there a simple
way I can fix whatever happened? Or will I have to reinstall cygwin from
scratch? If anyone can point me in the right direction for understanding
what happened and how to fix it, I'll be grateful. I don't know much about
the interaction between cygwin and windows, I just use it for compiling
and running C programs and some batch text-processing, so apologies if the
question is very basic.

Thanks --Jon Wild

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