Q: How can I reduce the box size in a project without starting completely from scratch
A: If you are using a recent version of EMAN2, it should be possible to go back and change the box size, but doing so may be somewhat messy, since as you work back forward, you will be displacing some, but not all information from the earlier box size, and invalidating many of your earlier results. For example, the structure factor computed at one box size will have a different sampling than at another box size. Most parameters can easily be changed during a project, but box size becomes quite messy, so, while it may not be required, I generally suggest to people that if they want to change the box size they start over with a fresh project, by copying over the particles from the first project with the new box size.
That said, 500 to 296 is a pretty significant change. The recommendation for EMAN2 is that the box size be ~2x the smallest possible box that would fit the particle. Clearly I don't know what this size would be for your particle. If you are having centering issues, two tricks may help. First, you can use a small box size when picking the particles, and only increase it to its final value when you 'generate output'. Second, you can change the box display in boxer to show a dot in the center of the box as a visual cue for better alignment.
If you wish to copy particles from one project to another with a different box size, I would suggest exporting the particles from the first project as hdf files while shrinking, then importing these into the new empty project. For example, in BASH:
for i in e2bdb.py particles --filtexclude=ctf do e2proc2d.py bdb:particles#$i <path to new proj>/$i.hdf --clip=<newsize>,<newsize> done
then run e2workflow from <path to new proj> and import the hdf particle files (after which you can delete the hdf's)