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it depends of course what changes you intend to make - if you're going to add partitions, change which OS boots etc, then the likelyhood is no, it would not be a good idea.
We don't use that file for anything, but you may change Windows in a way which breaks other software (like EEPC).
I'm trying to add the /PAE switch to the boot.ini. Do you think that would corrupt anything?
nothing would indicate so, but it's not something that is tested AFAIK. W2003 running EEPC as a client is very uncommon.