Lachlan, You can feed expedt an input file which contains whatever keystrokes you would normally give to the program. In theory it would be possible to set up a batch file for a cascading refinement, but you'd need a lot of work to make it intelligent enough to figure out which atoms to let go at what time. It would be possible to write a helper program which could figure that kind of thing out for you, but then you'd be looking at a black box, which I don't think is welcome in the powder community.
Every problem usually has it's own quirks.
As for convergence problems, it's worth playing around with the damping until things settle a bit and then reducing the damping factor. It depends on your data and space group, but 100 atoms in the asymetric unit, all with 3 xyz's suggests you'd need around 3000 peaks to get a 10 to 1 data to parameter ratio. That's a lot. Frequently you can get away with refining with a subcell or higher spacegroup than really applies, then look at your structure as a distortion of the one you've got converged. Convergence strongly depends on the data quality.