I think my original reply to you must have gone somewhere in cyberspace, so I'll try again.
I don't think there is any "global" way of deleting your flags. You will have to go in individually to delete them, just as you went in individually to create them. However, you can do a Search and create a list of where they are and that might be helpful.
Go to Search/Individuals/Flags (you may want to later search for Events, since there are flags for both). You can create a grouping and for each flag make sure you ADD to the list. Once you have all of your flags grouped, you can go in and create a list (perhaps our site on creating a list can help you at http://rug1.tripod.com/page12p.htmlhttp://rug1.tripod.com/page12p.html) print the list out and then start your work from there. I have actually found the flags I use to be quite useful; others do not. If you ever plan to go to TMG, I believe the flags are not used, so you might just want to wait. Otherwise, I wish you the best of luck with all the deletions. :)