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I was doing Instructor #5 (Sauromaugue Champaign). I died, warped to HP, and went to Adoulin to farm a gnatbane for a friend. After that I changed jobs, went back to the burrows via the warp npc in Upper Jueno, and traded him my grimoire. On the selection screen, my only options were Adjunct #1 through Researcher #1... All of my progress was gone. I can still buy the Rewards for the areas I had clear, however.
That's normal, your progress is wiped after doing any boss in meebles, whether you succeed or not.
That's actually working properly. To get a spawn for a boss (which is Expedition #5), you are asked to turn in your grimoire, and upon finishing (either winning or losing) the expedition, you're given a fresh grimoire with no progress on it. It's just how Meebles works. You work up a tier and get to the boss, then start at a new tier, repeat. The only thing that carries over are clears for reward purposes (all Rank 3s, etc) and KIs won from bosses (which are lost when you get a spawn for the overall zone boss).
Edit: Sniped. :( Beaten to it.
Well now I just feel foolish. :( Thank you for the replies, though.