Hi,
This is not a question, rather an answer in case someone else would have the same problem.
I had a strange behaviour : if I scraped snes games for example, everything was fine. But if I tried and scrape megadrive games, everything seemed fine, but none of the scraping was saved and when I would come back to emulationstation later, I would not see any image nor any game information for the megadrive games.
For snes I didn’t have this problem.
After searching in folders and files, I discovered that at launch time emulationstation would output many error messages about the gamelist.xml file (/home/pi/.emulationstation/gamelists) of many systems. Among them the megadrive…
The problem was that the file in those systems was totally empty, when it should have been with the XML header and an empty gamelist tag.
So I copied a correct one from another system to all the erroneous ones, and then everything was correctly saved when I scraped :-)