When you edit the disk there is no locking: you bypass the filesystem and OS. If you can write to the disk, you can do it. In fact doing this is the best method to avoid dataloss.
What most probably happened is that someone or something wrote gibberish in that directory. That means the directory's entries point to wrong FAT entries now however. FAT entries which already belong to other files, creating crosslinked files. And depending on the chkdsk program used it might delete or rename or whatever ALL "crosslinked" files: both the file inside the directory and the files from the outside, leading to data loss.
If you simply mark the directory as deleted with E5h, then all you have is a single lost file (the directory) and all other files on disk are untouched.