It was the God darn Flatpack! (ﾉ °益°)ﾉ 彡 ┻━┻

Thanks to the answer here (Java error creating Path from String, does linux limit filenames to 8bit charset), I managed to figure it out.

To test it, I created a basic Java project in IntelliJ with the following code:

import java.io.File;

public class Test {
    public static void main(String[] args) {
        File f = new File("\u2026");
        f.toPath();
    }
}

Whenever I ran it via IntelliJ, I'd get an error: Malformed input or input contains unmappable characters: ?

But if I were to run it via terminal using java Main (after compiling it with javac Main.java), it ran fine. Without even the LANG variables.

In the Flatpack IntelliJ version, I was getting this message in the console (which I kept missing cause it was always hidden because of the rest of my System.out.println() output or the errors - with which it blends real nice)

"Gtk-WARNING **: Locale not supported by C library. Using the fallback 'C' locale."

So I downloaded the .tar.gz for Linux from IntelliJ's website, ran it via terminal ($./idea) and what do you know? The warning wasn't there.

I tested the sample above by running it in IntelliJ and it worked fine. Didn't even need the VMOptions or anything.

So I opened my project and all of the code described in the original post worked as expected.

No ?????, no ����� and it even created the files described in the MainController.java file properly.

I spent 2 days dealing with this issue...