The standard way is to redo the refinement with iters 0 and the scale factor of the phase you want to exclude set to 0.
It's obviously a pain to do this by hand in a sequential refinement.
If you're doing the sequential from a .bat file you can easily do this with #ifdef #endif flags in the INP file. Basic idea would be to do each refinement twice. The first time you refine as normal. The second time (iters 0) you do the outputting. You'd tell topas what type of refinement to do using commands like the ones at:
http://topas.dur.ac.uk/topaswiki/doku.php?id=automating_multiple_refinements