Sorry that we missed responding to this, but I thought it was still worth addressing this issue for anyone that is interested.
First, to clear the notes field, run the following statement using the SQL Workbench (In the Legacy database, under Admin > Database Utilities. In the Windows App, under Tools in the main menu bar): Update person set Notes = null.
Warning!! This will clear EVERYTHING in the Notes field for EVERYONE in the database. If you have concerns about this, please contact customer support for assistance.
Second, if the "Non-parent Pickup" field is mapped during an import, the new information will replace the old information for those members that are imported. It does NOT clear the information for members that are not included in the import. I'm wondering if it would be helpful to include an option during the New Year Setup to clear that field, similar to the options given for clearing the permission-related fields.