Is it possible to open 2 or more projects, in different IntelliJ instances, and debug across them?
For example: I start debugging on Project A. Project A calls a method in Project B. I want my debugger to continue on Project B on the other window.
I know a way to debug across multiple maven projects, is to add all the projects to the same IntelliJ instance. But I would like to know if there is a way to do it, without adding all projects to the same instance. To break up the projects in its own IntelliJ windows.
Yeah it is possible
First create a remote debug configuration: Edit configuration -> Remote.
You will see a command line argument which you have to copy and paste it to the script that you made to run your java file. 
Keep in mind, to make sure your Project B doesnt starting running before your turn your debugger on, change suspend=n to suspend=y.
Once your parent java file runs go to the secondary idea window and run the remote configuration that you created in first step. If everything is right, your code will stop at the breakpoint.