Only delete files you own...

[Laie]

With dozens of saved games in my folder, merely bringing up the "load game" dialog can take a good long while. So I decided to move them out of the way. Conveniently, there already is a folder named "Backup" so that's where I put my old saves.

You aklready know where this is going, do you? When I came into the situation that I needed one of my vintage savegames, I looked into the backup folder and found... several "persistent (date,time).sfs" files but not a trace of the .sfs files I moved into that folder. A few configs that got moved as well are still there, I take this as a sign that I'm not imagining it, that one day I really marked everything and moved it to the Backup folder.

Apparently KSP zealously rubs out any extra sfs files in the backup folder, even if they do not match the naming convention of KSP's backups (and hence are in all likelyhood none of the automatic backups). Would be nice if this could be changed.

[Kerbart]

I'm sorry for your loss, but one can in similar fashion argue that you shouldn't be placing files (and subfolders) in folders you didn't create, even if it is convenient. A simple solution would be to make a folder "laie's backup" and put your files there.

another solution is to convert the saved games (folders, really) into zip files and leave them in the saved games folder, if you're after such convenience. I do the same with mods I want to temporarily disable.