To re-install CHARMM, eg with new arguments to
rm (or mv) exec/<machine>/charmm
rm lib/<machine>/*
rm build/<machine>/pref.dat (if you made changes to pref.dat that you want to keep, don't do this step!)
rm build/<machine>/Makefile_<machine> .......

Changes to the main makefile should be made to build/<machine>/Makefile_<machine> (not to build/<machine>/Makefile), in which case you should not remove it.

After a source-code change it should be sufficient to just do ... (with the same flags as for the original installation).

Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden