When changing layouts, all the necessary resources for the next layout are loaded into memory. If the amount is significant, this can cause a freeze during loading/changing layouts.
To prevent this, you'll need to load the assets needed for the following layout during the current layout, since assets in use for both layouts are not unloaded from memory when changing layouts.
I would try do this by using load sprite from url. I believe you can also create the object that wasn't originally placed in the layout editor to load it into memory, but I'm not sure.
As you load sprites in, assuming you don't try to do them all at once in a single tick, your animation should still play. Change layouts after you've got everything already loaded into memory.