Transparency and flattening

I'm using AI CS3 on PC. I've been given an EPS file that was apparently created in AI 11 on Mac. It has no preview (at least not that will show up on PC).
I opened the file in AI to save it with a preview. When I do a Save As, AI says:
"When spot colors are used with transparency, changing them to process colors outside of Illustrator can generate unexpected results."
Does this mean I need to change all of the spot colors in the file to CMYK? The file has been used as-is in the past apparently with no repercussions.
Then AI says:
"The document contains artwork that requires flattening."
What should I do? I find the whole business of transparency and flattening confusing.
I COULD just use the original EPS file as-is, but I really hate not having a preview.
FWIW, the EPS will be used in an existing Quark file.
TIA,
Marlene

The first message is just a warning. If you intend to keep the spot color(s) on press, there should be no conversion to process involved. If there is going to be a conversion down the line, you're better off dealing with it within Illustrator. That's what the warning is trying to tell you.
My guess with the second message is that it has to do with the improved transparency flattening options in newer versions of Illustrator. The document uses transparency, and that means flattening is required (because PostScript does not support transparency).
I would just let Illustrator do its thing and save out your new EPS with the Windows-compatible preview. If the file was used in the past without problems, you probably don't have to do anything within Illustrator. However, if you see a lot of transparency features in use, you might want to flatten more aggressively, even if that means further tipping the balance away from vector toward raster and ending up with a larger file.
The preview really won't tell you much (other than position) once in Quark, so make sure you output a proof -- at least to Adobe PDF. Check to make sure each spot color in your Illustrator file goes to its own 'plate' out of Quark.
Recommended reading: http://www.layersmagazine.com/illustrator-render-photoshop.html

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