How do I open the project.binary file?
Via the Hex editor.
But seriously, the file name says .binary, not .godot, this means that the file was converted from text to binary during export.
At the moment, you need to use other tools to change this file.
Perhaps I will add the ability to convert this file to text, if possible. This would be just as useful as restoring .ctex (which cannot be restored currently either).
gdsdecomp is trying to decompile everything. It sometimes works, but it does it extremely slowly.
I am currently exploring what I need to convert binary data from Godot and the main problem that I have now is to port the marshaling code (and all types of godot Variant…). After that, I should have enough tools to restore project.binary to the project.godot.