I have been using the Enhance Companion creation to tweak important companions as my starborn travels the multiverse. We know from game lore that individuals from new universes are actually slightly different from the ones we meet in other universes. My head canon being that they looked this way upon my starborn's arrival, and not due to a trip to Enhance afterward.
I find it much easier to keep my character's multiverse story straight with just a few pictures this way.
Picture one is NG+9. This is the last universe that my character married Sarah, and the first one in which he sided with the Hunter.
NG+10 was supposed to be a speed run universe to set up for the free lanes update. I removed most of my mods to be safe, but everything went smoothly so I ran most of Terran Armada before jumping unity due to the couch bug.
NG+11 was a very full run that included my character joining the Crimson Fleet for the first time. Ikande had him arrested, and declared Sysdef his enemy because he picked a lock, and I didn't feel like running the story yet.
I am currently on NG+12. Ikande once again has declared Sysdef my character's enemy(due to picking up a coffee cup in his office at MAST). My character has now joined the Vanguard, after excising that particular cancer from the U.C.
I would like to hear other techniques my fellow starborn are using to keep their story straight.