The quick resolution to this problem is to backup your site with All-In-Migration or equivalent plugin before proceeding.
Make sure you have updated “The Events Calendar” master plugin. Next deactivate and delete old PRO version plugin files which will clear existing folder from your stack. Now install the 4.1.1 Pro Update. Problem solved!
I don’t believe this is a problem unique to TEC as many other plugin installations may face the same issue not wanting to overwrite existing files or folders. Just make sure you backup your complete site before attempting just to be on the safe side.
Keep up the good work guys!