In the future, you might start your projects by creating an "object bank", which is simply a layout that isn't really used for anything except to hold your global objects and to keep a copy of objects you want to spawn/create during the game (to get around the limitation that there must be at least one copy existing somewhere.) So your audio, arrays, etc. would all go here as well as an instance of every object that doesn't appear at the start on your layout.
All very well and good, but you need to solve your current situation. Here's how I'd do it:
1) Backup your game, and, working with a copy,
2) create a new empty layout with all of the layers in your existing prototype layout, and name it Template
3) lock all of the layers in your prototype layout and one layer at a time unlock the layer, select all of the objects on the layer and paste them in the corresponding layer on the Template layout.
4) When all of the objects are correctly in place on the template layout, set its event sheet and test it.
5) If testing goes well, use the Template layout as the starting point for your new levels. You can keep the original prototype level as it is, or delete all of the unnecessary objects from it and rename it "Object Bank".
6) When you finish your game, you may want to delete the Template layout, or rename it and use it as your last level.
Hope that helps!