If you are sure the option field in the db for your sidebars isn’t corrupted, then it may be a clash in the way you’ve named (id’d) them, or perhaps in where you have your hook to create them.
It’s impossible to say without more information, or someone taking time to walk through your site, examine your code, and test your db pre and post upgrade, etc
[Edit: I’m assuming you’ve also gone through an upgrade with all other plugins deactivated, and using the bp-default theme, to ascertain whether that preserves the widgets, before switching to your theme, and reactivating the other plugins]
