You could either create a new custom css file and link to it from your style.css file….or keep all your edits in a custom section in your style.css file and make sure to copy/paste it in the new updated version.
Function files usually don’t have that much done to them, so I would just keep a backup of it and add in any changes you made inside the new version.
I’ve seen this site – http://www.diffchecker.com/ recommended here as a way to check two files to see which lines have been changed/updated.
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