Should you delete your Saves folder when reverting to vanilla Skyrim if you want to retain those saves?

I have installed a load of mods over the past few weeks and now have a much clearer idea of what I want to keep and what I don’t. My /Data folder is a mess as a result.

I was considering doing a clean install but I came across this guide, which apparently gives you the same result, but you don’t have to re-download several gigabytes of data, you just have to be careful and methodical about what you delete.

The guide says, in step 11, to delete "all files and subdirectories", from My Documents/My Games/Skyrim which would include the Saves folder.

What is the point in deleting the Saves folder if one wants to keep one’s saves? Surely it should be left [and backups made, just in case].

FYI I am on Linux, I don’t know if that makes any difference. I don’t think it does, apart from the fact that the Saves folder is – for me – in

/home/user/.steam/debian-installation/steamapps/compatdata/72850/pfx/drive_c/users/steamuser/My Documents/My Games/Skyrim/

rather than

 C:/Documents and Settings/user/My Games/Skyrim