> I do not have the ssl enabled in httrack.

Note that recent 3.30-RC release fix this problem (the SLL 
module is correctly detected now)

> The problem 
> is, httrack is trying to access the link on the original 
site as '//
> www.bla.com' and thus gets a 404 - basically, it ignores

Add this filter rule:
-https://*

that is,
httrack '-https://*' www.example.com ..