Another problem: I have custom spot color that has been imported from illustrator file.
When I change the color in Illustrator, InDesign does not update the color.
Why? How can I redefine spot colors imported from external files?
Haven't had a chance to look at the first half of your question yest, but if for the second half either redfine the swatch in ID or delte the art, then delete the swatch, and re-Place the art to bring in the new swatch definition.
I'm not sure what you are doing, or waht's happening, but I've crashed three different machines running 6.0.5 (haven't installed 6.0.6 for reasons related to a book revision I'm working on with linked AI files) trying to export a test book with two docs containing Pantone Swatches aliased to another color. I suspect this is a bug, and ifg it wasn't fixed in 6.0.6 it's very unlikley it will ever get fixed.
The same files work fine in CS5, where the behavior is that whatever the ink alias settings are in the synchroization source file will be used throughout the book unless you set something different by invoking the ink manager in the export dialog.