Thanks for opening the new bug...makes sense as good way to handle it.
As far as the warning when you upgrade, I didn't see any errors during the database upgrade (all screens in the browser at the bottom and/or top said completed successfully). While it's possible it may have given a message in the middle of one those screens, they are very long (I'm presuming just going by the "completed successfully" message at bottom before clicking "Continue" is considered best practice?).
Of course, this isn't an issue for me anymore fortunately.
Going into the database to find the rqp question types to remove them would be beyond some people though I believe.
I'm seeing these errors when I visit the question category page using latest HEAD:
Table 'moodledev.mdl_question_rqp_types' doesn't exist
SELECT * FROM mdl_question_rqp_types
line 677 of lib/dmllib.php: call to debugging()
line 601 of lib/dmllib.php: call to get_recordset_sql()
ine 569 of lib/dmllib.php: call to get_recordset_select()
ine 862 of lib/dmllib.php: call to get_recordset()
line 172 of question/editlib.php: call to get_records()
line 514 of question/editlib.php: call to question_list()
line 59 of question/edit.php: call to question_showbank()
in /moodle/dev/lib/weblib.php on line 6177, referer: http://dev.moodle.com/course/view.php?id=2