In December 2014 there were heaps of posts in various places about follower abilities being randomised after a faction change.
Probably the biggest "bug" on the list, ALL your followers abilities and traits get randomized, even the neutral ones. Followers always have 1 predetermined Ability and 1 predetermined trait and the others are random depending on what quality your follower is. All followers keep their quality, level and Ilvl but the Alliance specific ones get turned into their Horde counterpart. These followers are pretty much never the same class on both sides and have completely different main abilites so these are pretty changed (Understandable) but their other traits/abilites are also randomized.
- Krabban (source: Reddit)
However, ALL of their traits changed.
I had some really good lineups, now half of my epic followers are useless.
- Tassit (source: Wowhead)
I now have 12 followers with "Danger Zone" ability and only one with "Wild Aggression". I had 3 Scavenger trait-followers but now only one.Bodyguard reputations reset, I no longer have any rep with any bodyguards.These problems are the ones I have noticed so far.. I'm so sad.- Quickwitted (source: Reddit)
From Blizzard WoW Support, the article on Faction changing says (updated 25 March 2015):
Your followers and completed Garrison buildings will not be lost.We had a new boomkin transfer over from Alliance yesterday and he said all his traits were preserved. He was worried about losing all his epic mount, scavenger and treasure hunters, but when he checked his followers, he still had the same amount of traits that he had previously - obviously all his followers were converted to the Horde equivalents.
Unfinished missions or buildings, or incomplete work orders before changing factions will be lost.
Faction-specific followers are replaced by an equivalent follower from your new faction. Follower traits stay the same when changing factions, but follower abilities may change.
So that is a big relief! So now you can safely faction transfer and keep all your traits.
One other thing about followers:
For Harrison Jones and Garona, they have set traits (Harrison has Mentor and Garona has Master Tactician). These traits are NOT rerolled with a trait randomisation. They are permanent. I rerolled the traits on Garona today and still kept my Master Tactician.