"Le père de Spinoza semble lui-même un sceptique, qui n'en tient pas moins un rôle important dans la synagogue et la communauté juive."
first point: tenir un rôle moins important d'être sceptique text, this is implied and allowed by transposition according to French grammar
second point: there's the de, in this case, d' calling for the en.
third point: the negative then becomes: n'en tenir pas moins un rôle important
Spinoza's father seems to be a skeptic himself, who does not have, due to this, a less important role (to play) in the synagogue and Jewish community. This translation is only to show what happens to the en.
I think the en follows the rule here in fact. It just has to be transposed for it to appear: d'être sceptique, this or that happens. The en refers back to or "recalls" that phrase, which is implied.
d' + être + noun is due to.
c) De introduisant un inf. suj.;de signifie « le fait de », en parlant d'un fait particulier, ce tour littér. est assez répandu (cf. infra II B 1).
http://www.cnrtl.fr/definition/de