Q: How can I reduce the box size in a project without starting completely from scratch

A: You don't need to redo particle picking, and you can use 3D maps generated at the original size as initial models for the new size. You need to:
 * return to the "generate output step" in particle picking and rerun this with the new box size
 * rerun automatic CTF correction
 * you should not need to rerun 2-D class averaging or initial model generation as long as you got a reasonable initial model at the old size
 * run new refinements with the newly reboxed particles