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How can I save customized orientation in one *.c3di file and apply my customized orientation in another *.c3di file?
As far as i know you can not. I just went thru this where I have 7 assemblies that have all the same parts except one main frame part is replaces and that moves all the other components to their new locations. I created a bunch of animation sequences for this and then wanted to duplicate those on the other assemblies, i could not find a supported way to do it.
Here is what i ended up doing:
The key step above is always doing this in the same folder location. Illustrate apparently uses absolute file paths to locate the linked source file. So you need to rename your new file and have it in the location Illustrate is expecting or it to update.