Hmm, I'm not quite sure if the following is what the OP had in mind for FLWM, but rm -rf ~/.wmx is a "most brutal" way to "get rid" of pretty much all FLWM menu entries.
Now to re-establish the "SystemTools" one could use flwm_topside_initmenu and to get the menu entries of all installed extensions back I'd try my luck with: ls /usr/local/tce.installed | xargs -n 1 flwm_topside_makemenu