Affinity changes the faction of a character when they come into the squad (that's in the glossary for Affinity), so yes. Most (maybe all) other ways of bringing characters into a new faction do not change the faction of the character. For example, GARY's CE or Disra's CE. So if GARY brings an Imperial trooper in, it cannot benefit from the Sith trooper CEs.

Affinity definitely changes the faction.



You're might be thinking of a couple other rulings related to Affinity.

One is the Frozen in Carbonite ruling. If you use Jaina to bring Han in Carbonite to the New Republic, he can only thaw into a New Republic Han Solo, not a Rebel one. I tried to understand exactly how Frozen in Carbonite works and why it was ruled that way, but I couldn't fit the ruling into my mind's framework of understanding the rules, so I just consider that an exception. Fortunately, Frozen in Carbonite is kind of its own animal so it doesn't really serve as a precedent for anything else.

The other is Garm Bel Iblis and the Yuuzhan Vong Ossus Guardian. Garm can bring Rebels or New Republic in as Reinforcements. He could bring a YV Ossus into a NR squad since the Ossus has NR Affinity. That affinity allows it to go into an NR squad and then it would have its faction changed. However, if Garm were in a Rebel squad, he could not bring in a YV Ossus Guardian. Garm can bring in NR pieces, but the Ossus is a YV piece. The Ossus' affinity allows it to be in an NR squad, not a Rebel squad. The Ossus would have its faction changed to NR, but only if it were in an NR squad. It is naturally a YV piece, and thus not eligible to be in a Rebel squad with Garm. (Hopefully that made sense.)