Well if you changed the folder names then just change them back. For best of cases you have your project under version management and can easily get back to the previous version by checking out previous versions from git.
Concerning the live website – it can update if you change md-files but it might only read html-files (those from layout) and especially Julia functions upon first serve – that is why you sometimes should restart that (for the details which parts are dynamically loaded and which ones are not precisely I am not the expert). Also please read the links from Thibaut about the general workflow with Franklin.
And without an example what you tried it is still complicated to help. And please also consider Please read: make it easier to help you concerning this remark.