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There are two ways of doing this that are covered in detail in the manual under the "Special Topic - How to Edit An Illustrator File and Getting the Software to Use the Changes" section.
There is the Reload option and the Replace option. The Reload command must be prepared for by the file originally being opened with the "Open By Layers" option checked. This would allow you to make changes to the same Illustrator file and then use the changes.
The Replace option will allow you to replace the Illustrator file being used with another one, without having to do any preparation.