I made a logo animation with paths, masks, illustrator file, etc.
A day after, when reopening the file, my animation completely changed. it looks like my masks aren't connected anymore. And my illustrator file is still linked but it changed the position of the assets in AE but my illustrator is still the same.
That's not realyl useful in any way. Show us screenshots and provide exact info about how the files were created and imported, how they are used and so on. A simple re-save of an AI file after its initial import can cause this, which isn't AE's fault at all, just AI's long-standing behavior of not persistently handling group data and transform info plus bugs in artboard handling.