What is the best way to rebuild a website?


Lets say I got 2.1.3 installed on my main domain and I feel that some files might be missing or something might not be installed properly so want to rebuild everything without effecting the DB or my skin (my main problem is that thumbnail images are not alway generated to the correct size)

WOuld the best method be to install the same version from scratch on the subdomain, make a copy of all the files, then delete all the files on the main domain (apart from the skins folder and images) and then upload the copied subdomain files (minus the skins folder and images folder)?

I take it that this is the best way to rebuild a site? I have highlighted that the skins folder and images folder should not be touched are there any other folder or files that also should be left alone?