Sorry if I was unclear, but yes, I have done exactly what you mentioned, multiple times.
I wanted to try something: I deleted the entire folder where all these e-mails used to be. As I mentioned, according to Recuva, these files had been previously overwritten by other files which were newer e-mail (.eml) files in that same folder. Now, when I delete this entire folder including these new files (After backing it up externally), run wipe free space after that, finally Recuva finds no trace of the previously deleted files nor the new files which I now deleted.
It seems as if those new files overwriting the old (previously deleted) ones somehow prevented the traces from getting removed, if thats even possible...?
Either way, now they seem to be unrecoverable as there is no trace after WFS. Now I ran a Recuva scan on the external drive which now contains the files, and it shows no recoverable files. So it seems like I've finally gotten rid of them. I don't even know how / why though, if some one has an idea, I'm curious to hear.