A careful comparison between your original file and the modified file should show the difference. Did the template you are using come with an includes/templates/YOUR_TEMPLATE/templates/tpl_shopping_cart_default.php file? If so, that means there were changes made to the default file which is why it's in your overrides directory and by just dropping in the file that came with save for later you lost the customizing that your template's file has.

If you don't have a comparison tool yet, I would suggest winmerge, it's free and easy to use. You need to merge only those parts that have to do with save for later, sometimes there are other differences to do with using different version core files or other changes that have been made for other mods or templates.