Companions since KOTFE are essentially duplicates of their original versions. However, there's some significant (and annoying) changes.
Firstly, companions like Torian and SCORPIO had their combat styles changed from dualblade to rifles. This means that any dualblade weapons that were possible to use on these companions no longer work. Such as giving the Mandalorian Beskar Spear to Torian.
Additionally, all duplicate companions no longer approve / disapprove of choices made in Flashpoints, nor do their mouths move when speaking to them.
Some original companions (such as Mako) are available for recovery at the companion return terminal, allowing you to keep the original versions of these companions as well as the duplicate version.
Is it possible to get this functionality added for all base-game companions? I would very much like to give Torian and SCORPIO their dual-blades back.