Bringing very complicated Illustrator files with spot color into ID?

I'm putting together the files for printing the first collection of my current comic book. Normally I'd just output 300dpi TIFFs, but I'm using a spot color overlay in this project.
Does anyone know the best way to get this into InDesign with the spot color intact?
These are SUPER COMPLICATED files, and experience has taught me that just saving a PDF to drop into InDesign results in a note from the printer that the file refused to print. I also can't do tricks involving moving it into Photoshop and selecting one particular color to put onto a new channel, as there's a lot of overprinting going on.

I think maybe you should check with other printers, as well.
Bob

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    ...which to a designer is completely insulting...
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    Paolo Tramannoni wrote:
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    Paolo,
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    Bernd

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