I would say it is definitely doable. I imagine it will take a lot of testing and time to make sure everything works, almost certainly more than the 'average' game.
I imagine one of the hardest parts will be parsing all of it and making it compatible with your scripts. Other than that, right now I cannot think of anything that would be necessarily impossible to do with Godot. All of the other parts are, more or less, doable so long as you have lots of time (and potentially do not mind using GDNative if GDScript/C# does not work)
If you want to use Godot to save/load custom scenes at runtime, then you could try to use something like the DSCN plugin I made. It is not very efficient, not at all secure, and creates pretty large files because it stores everything the scene needs in the file, but it might give you an idea on how to save and load custom scenes to and from binary files.
The plugin allows you to save and load meshes, sprites, labels, fonts, scripts, and pretty much everything else a normal scene can store. There are some issues and I wouldn't suggest using it in production, but maybe it will be of some help :smile: