I have this same problem; I keep my gold-upgraded Life/Ninjutsu equipment on Kabuto always, but when I replace him with Sakura for SA she might get it, or Kiba might get it, or my main might get it. When my main does I can't just re-drag ninja; I have to go into "Character" and move every piece around, which is time-consuming and especially difficult when equipment looks the same ("Kage Hat +1", for example) but has different magatama/refines behind it that I want on a specific ninja.