I wanted to share the method I used to change my game save from an older version of the mod to the latest. This procedure was mostly explained by Commando5551 first, I'm just offering a tidy step-by-step summary. Also, be sure to check Matt Smith's video linked in the main page of this mod if you want to learn more about it.

1. Load your old save and make sure everything is tidy (bring back shop in a stack if it was laid out and remove players to repack characters).
OPTIONALLY: If you don't want to repack characters, you don't have to, just select everything in the character area, save a "Characters" object and delete what is selected before proceeding (there is a limit to what you can select at once).
2. Select EVERYTHING with a big rectangle selection and then Ctrl + click everything that is missing from the selection. This includes the game boxes, party sheet and even the map (the map saves with prosperity and Xs for completed and locked scenarios).
3. Right click on anything you selected (such as the main box) and "Save Object", give it a meaningful name.
4. Delete the map
5. Select every sticker on the map by CTRL + clicking, right click on any one of them and save a "Stickers" object.
6. Load the latest version of the mod.
7. Delete everything that you will be bringing from your old save. You will need to unlock what is locked to delete it.
8. Go to your "Saved Objects", click the 3 dots in the corner of your objects and click spawn. Do NOT just click the objects or they will spawn in the wrong location.

The only thing I don't like with that last part is that the first time you click a scenario number on the map, it will spawn a sticker even if there's already one. This will not cause any problem and they will not accumulate if you change versions like this many times. The bottom-left and global achievements stickers work as if you were still in your original save.

Hope it helps!