You could try to recover them with testdisk or photorec (don't be deceived by the latter's name, it can restore countless file types), but the best way to prevent data loss would be backups on a regular basis.

Testdisk and photorec are both part of the same installation package testdisk. Its installation is explained in the first link above.

Ok thanks a lot, I see what was wrong.
In fact I was lauching emulationstation from the .xinitrc file because I wanted to avoid using openbox. But is seem not to be possible. To make it as clean as possible I edited my files like so:
/home/pi/.initrc

exec openbox-session

This will start an openbox session in X and trigger the autostart file that i edited like so:
/home/pi/.config/openbox/autostart

xterm -fg white -bg black emulationstation -fullscreen

This will lauch emulationstation in a black xterm terminal in fullscreen which is used to display the file manager or retropie setup.

@Impman66 said in Is WinSCP or Putty necessary?:

So it begs the question, is WinSCP, Putty, or any other "file sharing" program necessary?

no, there are 3 supported methods of copying roms, and you're simply using the third: https://retropie.org.uk/docs/Transferring-Roms/#samba-shares

Update, I've gotten it semi working. Somethings wrong with my retroarch setup, the default bios directory is not the actual bios folder, i had to manually set it to that. Semi working because I can't seem to get retroarch to use global configs, i have to manually set each systems directory.

But thats not the topic of this thread. I guess for the time being this is a moot issue, the asterix dont seem to mean anything and arent causing the problem. Thank you all for your time.

I wonder if my issue stems from doing an update to retropie 4.4 rather than a clean image?

@pjft

Actually, they don't.

When I transfer via USB, the autocopy feature doesn't duplicate them. They only exist on the stick.

And when I do manual transfers in file manager (of bios or themes), I ignore them, so no sweat.

Okay, it looks like I have it running pretty clean now. Thank you all so much. Next I'll try to figure out how to add Famicom CDS, Super Famicom, Virtual Boy and maybe Game & Watch directories/roms to my build. Time to start hunting through the threads [slaps and rubs hands together in eager excitement] :)