If I am at 3 million fame; Plunder another 3 million.

Then loose that 3 million before update due to battles; Will I go on quartermaster if I lost the most?

Or will it be as I had never gained any in the first place?

I believe its would be like you never gained any : I noted that the figure seems to be the difference between today and yesterdays totals at reset, so any losses will offset any gains over that 24 hrs, and vice versa.