Watch the Old Gun sometime if you can find it and have a stomach for hard things.
Miracle at Moreaux??
Maybe either The Assisi Underground or Conspiracy of Hearts? I remember a wonderful movie, too, although I’m not sure it is either one of these. I just searched and came up with these two names. They both look good.
http://www.amazon.com/The-Assisi-Underground-Roberto-Bisacco/dp/6301966627/ref=cm_cr_pr_product_top
Another possibility:
The Scarlet and the Black with Gregory Peck and Christopher Plummer
http://en.wikipedia.org/wiki/The_Scarlet_and_the_Black
IMDB says Au Revoir... is based on an incident from Louis Malle’s youth.
Perhaps looking him up on IMDB and scanning his works might prick your memory?
This is a list of Holocaust films made since the 1940s and it should show up here.
http://en.wikipedia.org/wiki/List_of_Holocaust_films
Internet movie data base makes no mention of a similar film in this genre, and has pretty much all you could want on this film.
IIRC it starred Loretta Swit as the nun who ran the school.
Probably not what you're looking for but....
This was an excellent inspiring documentary about some of the few people in France who made the right choice in the face of the holocaust. A small town in the mountains that hid 5,000 Jewish kids from the Nazis"
http://www.washingtonpost.com/wp-srv/style/longterm/movies/videos/weaponsofthespiritnrhinson_a0a92f.htm
Debby does Dallas.
This sounds similar to a French (with subtitles) favorite of mine starring Jean Paul Belmondo. The title is Les Miserables, but it is set in the WWII setting and the Jewish daughter is placed in a Catholic school to hide. As the story runs there are parallels to the original story of Les Miserables.