Game Version: 0.5.18d
Operating System: Win7 64 bit
Changing the main character's (MC) eye color via the lab breaks access to their inventory. After you change their eyes, the MC vanishes from the character roster when managing gear/inventory. They never re-appear in the inventory roster, regardless how many days you wait. Other functions, like combat party and interaction, appear to continue to work normally for the MC.
This bug is likely because changing eye colors always takes 2 days, while all other lab actions on the MC take 0. Since the MC isn't handled like a normal slave they aren't supposed to be removed from the roster like slaves being modified or given guild services are.