There are many ways to reduce your Astral Reputation. I think what this is referring to with "Taking Paradigm Shift again..." quote is using Paradigm shift to change to a favorable Astral Reputation will NOT include said bonus. (The hit to your Astral Rep is a price of being a Hermetic Elementalist - forever!)
OTOH:
There is something you may not know about, given your long absence from Shadowrun. (I am assuming you played 2nd from your post).
Universal Magical Theory: Is now the prevailing magical line of thought and came out (If I remember right in the middle of 3e). The basis of this is that while magic is expresssive of the individual, if follows a universal formulae, and to this point neither Hermetics or Shamanics got it all right...
Basically, it was an "In Lore" reason for the condensing of magic, traditions, spirits, and everything else "mumbo-jumbo" into an easier rule system....
So now, Hermetics that used to just summon "Elements", now summon "spirits".....
And Shamans don't summon a Spirit based on location, but on its activity/type....
SO, the Astral Reputation that a Hermetic Elemetalist suffers could be from forcing his perception of an elemental on a Sapient Spirit.... and that stain remains even after he changes his views (Paradigm Shift)