Animation messed up after reloading footage (Illustrator file) in After Effects

Without knowing what you actually did we can't really tell you much. That said, this is no doubt much more of an Illustrator thing like layer alignment changing or groups and sub-groups losing names or likewise being affected by position changes if you're not careful. A quick thing to do might be to use the "reset transforms" option in Illu, but anything more will really require much more details.

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