Ensure you don't have any nodes/object being polled by that system -> manage nodes view -> select polling engine in "group by" drop down box and select that polling engine.
if you are moving to another system (install somewhere else), uninstall and that should remove from DB.
if not, run config wizard and point to new DB.
to verify removed or to remove cleanly, go to settings page and click on "polling engines". When nothing is assigned to it, it should ask you if you want to remove from DB.
check the DB at this point "select * from engines" and if the entry for that still exists, you should be alright deleting that row.
**** always perform a backup of your DB prior to doing any kind of work in it.
Drat - was over thinking it. Thank you njoylif!