A few days ago I was editing a Boff at Earth Space Dock. When I tried to change the rank pips of the Boff it wouldn't let me. I backed out of the edit menu to find that my Evelyn Savea Boff from my original crew on my Discotoon was completely over written by the Boff that I was editing. The display name all the way down to the character model were changed. The only place that my Evelyn Savea Boff wasn't changed was in the actual Bridge Officer menu and it was only her name that was the same. The "copied" Boff was there in her place.
A little while later I went to upgrade the Ambush Turret Fabrication Kit with one of the Ultimate Upgrades I got from the Key Bundle. It upgraded, then was no longer in my menu when I went to equip it. My Discotoon is at max level and the kit was not still in my upgrade menu or in the R&D inventory. I had to actually equip a separate version of the kit I had in my bank after completely restarting my console and logging back in
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1. Before attempting any modifications, put the BOff you want to modify into your away team, and beam down so that they appear and are "cemented" as themselves.
2. Keep the first BOff in the Tailor Menu (usually Evelyn, Tarsi, Elisa, or Kagan) and the BOff you want to modify in your Away Team settings.
3. Your first BOff slot should be safe from being overwritten when modifying the BOff that these steps were taken with.