I believe this is just one of the many expressions where, to quote Grevisse (Le Bon Usage, 14th ed., §679) “en and y have an imprecise value”, that is, they are pretty much impossible to analyze according to the rules that normally apply to pronouns.

It’s very hard to read this and not suffer from some “cross-contamination” from n’en connaître pas moins, “to know nonetheless”. It could be just a variant of it (by suppression of ne pas, which doesn’t change my conclusion above), but if it’s a separate expression, I don’t think I’ve ever run into it.

Difference in meaning, which you can see in the translation:

1) Mais si je ne formule plus ma prière, en connaîtrez-vous le délirant souhait de mon cœur ? =

**will you know about [find out about] ** my heart’s delirious wish?

Whereas:

2) Mais si je ne formule plus ma prière, connaîtrez-vous** le délirant souhait de mon cœur ? =

Will you know my heart’s delirious wish?

I simplified the sentence to make my point about the EN.

One is to know something and the other is to know about something.

En connaître, according to the TLFi, means être compétent pour juger.

− Spéc., DR., emploi intrans. [Le suj. désigne un juge et, p. ext.,
une assemblée délibérative] Connaître de qqc.; en connaître. Être
compétent pour juger.

(TLFi, II, C, 2)

So basically, en is part of this special and originally legalistic meaning of connaître.

And the general meaning of the sentence suddenly becomes apparent: if I no longer make the contents of my prayer known to you [si je ne formule plus ma prière], will you because of that be less competent in judging the delirious wish of my heart [en connaîtrez-vous moins pour cela le délirant souhait de mon cœur]?