Edit the newgan.log file with a text editor by deleting the line(s) which contain your newgen's uid and then regenerate the config.xml file. I've also deleted the uid reference from the original config.xml file but I don't think that this step is necessary.
Thanks for the response - this didn’t work for me but I did figure out another way in case anyone else sees this.
I went into the config.xml file and CTRL+F'd the player's UID. I noticed that a non-bugged entry looked something like this:
<record from="Caucasian/Caucasian1038" to="graphics/pictures/person/2000383289/portrait"/>
However, my affected player's entry look like this:
<record from="Caucasian/Central European9664" to="graphics/pictures/person/2000353848/portrait"/>
For some reason, the first half of part in bold had changed from Central European to Caucasian, which in turn stopped the player's face being matched with the player. I made sure it was the first half that had gone wrong and not the second by looking for picture Central European9664 in the Central European folder of the facepack, and confirmed it was indeed my player's lost face.
I just changed Caucasian back to Central European, saved the config.xml file and reloaded the skin in-game, and the face was back.
I took it a step further then and used find and replace for all entries of Caucasian/Central European and changed them to Central European/Central European, which in turn fixed all the other players who I'd noticed had lost their faces over the years (but ignored because they weren't mine haha). I've only noticed this issue affecting players with Central European faces so far, but it might affect others. Just fix the file path in the player's entry, and their face should pop back up.