Hi Jory,
I am using both android studio and AIDE to code a LibGDX project but unfortunately I couldn't get the same project to work.
Instead I have a work around which may help, but adds a few steps to your process.
Firstly I have two branches in git, one called [project_name]_aide, the other called [project_name]_studio.
Then on each branch I created the project using the relevant IDE e.g. on the aide branch I created the project using AIDE.
Then, I work in either IDE when I need to. When I then switch over to other IDE, I push my code to the branch, then pull it in on the branch on the other machine/device, then literally copy the entire folder of normally core/src onto a root folder. Then I checkout the other branch, and copy the code back in from the root folder.
That way I keep the project structure separate, and just copy and paste the actual code.
It's not ideal but it works for me.