Is there a program that can edit the S2 levelorder

You need to Migrate the levels, A pop up should come up when you load the ROM asking you if you want to migrate the levels.

 

I strongly suggest you migrate the ROM using SonED, rather than ESE. This way, it will open up in ESE with a data arrangement that is much more managable. Trust me, I ripped my ROM apart after using SonED. =P

 

Nemesis' guide covers level order, I believe.
ESE I can do level order.
It's also possib;e to do it "the hard way" in hex, which is what I prefer.

 

Probably, I don't know if SonEd and ESE are compatable.

Open the clean ROM in ESE, edit the level order, make an IPS patch, and patch a backup of your hack. That should work unless ESE moves the level order data (And I can't see any reason why it would, since the level order is a fixed size)

Or you could do it in hex, which is just as easy, if not easier (Easier for me, I know).

 

Wait, I just thought of something, when you make your patch, make sure you use a ROM ESE migrated the levels in as the base, and the one with your level order as the changes. If you try making the IPS patch with a clean ROM as a base you're going to run into all kinds of trouble with the levels.

 

That's very important indeed.

Alternatvely, you could see the difference in a hex editor between a migrated ROM and a migrated with level order changed, and make the same change to a clean ROM in a hex editor.

But the IPSing would probably work.