First...understand that, at any time...something can go wrong with the best plans/procedures of human beings on a tool such as a computer. Computers are electronic, complex, and impacted by things that might be considered inconsequential from a human point of view.
Using chkdsk /r, according to the following link, should not ordinarily result in any loss of data.
Chkdsk (nor anything else that I know of) is not designed to fix/repair every circumstance imaginable on a system. It's a tool which can positively effect beneficial results for many computer situation. It may not be of any assistance to you, it may help. It should not make anything worse than it currently is.
Graphical Version of Chkdsk[/post]
Please skip down to the section dealing with the Graphical Version and ignore everything else on the webpage.
For you to ask me how to "recover" files from a hard drive I don't have...that's asking a lot. Let's run some tests on the drive first before we try to recover files which you claim are not visible.