I found a Empty Healing Kit, Master-work and tried to put a healing herb into it from the light healing kit I have. The master-work kit deleted itself.
Did you possibly combine your herbs in your masterwork healing kit into a regular healing kit without realizing it?
I did this once as well, not the first person to do this and won't be the last.
When working with healing kits, you need to operate the unique power from the one you want to keep.