To re-install CHARMM, eg with new arguments to install.com:
rm (or mv) exec/<machine>/charmm
rm build/<machine>/pref.dat (if you made changes to pref.dat that you want to keep, don't do this step!)
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 install.com ... (with the same flags as for the original installation).