@leighw14213429,

This was an Animate bug that was recently fixed by their latest 23.0.1 patch. Try upgrading Animate to the latest version and let us know if you are again able to import .FLA files into After Effects.

@Byron Cortez .FLA files are different from EOL'd Flash files. After Effects supports importing .FLA files as layered SWF animations by having Animate render the layers in the .FLA to individual SWFs.

- John, After Effects Engineering Team 

It says here that After Effects does support importing Flash files but with some limitations, that could be what is causing the issue.

Supported file formats | After Effects

Adobe Flash Player EOL General Information Page