I just wrote a similar script with the commands you just mention. And I tested it with messages in the recovery database, and they were still there when I brought the site back up. You should be fine. This is what I ran:
hcisitecleanup
rm $HCISITEDIR/exec/databases/vista.taf
rm $HCISITEDIR/lock/*
hcimsiutil -Z
hcidbinit -if
keybuild rlog
keybuild elog
dchain rlog
dchain elog
rm $HCISITEDIR/exec/sem*
