This script allows you to apply scale to all of your objects including linked duplicates. It will keep linked objects linked, lattice deformed objects deformed properly, and will even correct modifier values so objects with modifiers like bevel don’t look different after applying scale.
To load in the script in your own blend file, just open the text editor window and open the py file. Alt + P while hovered over the text editor runs the script.
Let me know if you like this script or if you encounter any problems with it. I know the coding’s not the most efficient, but it gets the job done and I’ll update this in the future.