Yeah, if you could zip up the madb and the logs and email them that could be interesting when I find a spare moment.
Derby has a MySQL like language, and you could just give the directive 'delete from userEvents' to whatever your tool is.
Another possibility is to port the database into MySQL so that the better toolset is available. Mango has the ability to perform that database port (can be found in the "convert database" type fields in your Mango/classes/env.properties (or Mango/overrides/properties/env.properties if you overrode it) which you just boot with the first time and it should port everything, then modify the environment to use the MySQL. I wouldn't expect an issue in the conversion since it seems the IDs have just [somehow] gotten jumbled and inserts are failing. Doesn't look like your database is wholly corrupted or cannot be read, and it'll convert the whole database before it goes about its other business.
Edit: I'm beginning to wonder if I'm mistaken, and if only the pointValues table is converted...