There were important communities in Bordeaux, Bayonne and various villages in south-west France but, for most of the period that interests us, these communities lived as public Catholics. Information on them can be found in relevant regional archives and Church records.
I believe the relevant archives are:
Archives départementales de la Gironde (includes Bordeaux)
Archives des Basses-Pyrénées
Archives municipales et départementales – Ville de Bayonne
The Gironde archives cover Bordeaux.
http://gael.gironde.fr/results.html?base=ead&cop1=AND&champ1=extfulltext&query1=culte+israelite