Orphaned files/folders left after upgrade

[Linuxweb]

Hey Everyone,

So after the upgrade to 7.6, I noticed that there were quite a few orphaned files and folders. As an example. I have customised the font size on the text editor for WHMCS when composing mail messages to clients. The font size was originally just too small for my ageing eyes. In the following folder is where I had customised the css for the font size:
/assets/js/tiny_mce/themes/advanced/skins/default/content.css

After the upgrade I see in /assets/ there is now a tiny_mce as well as a tinymce folder

So I downloaded an original copy of 7.6 and found that tiny_mce has been replaced.

So the question I have is what is the best way to go about clearing up these orphaned file and folders. Do I have have to manually navigate to each folder and compare file quantities and sizes, or should I just delete everything except my config and re-upload an original version? What will then happen to all my addons installed? or do these need to first be un-installed

P.S. I have made a full site and DB back, so I am not afraid to go full Rambo on the install. 🤣 I would just appreciate advice on the bets course of action here