Here's a (long) short explanation...
When you perform a Ubuntu upgrade, it disables all of your "foreign" sources, on the assumption that they may cause problems with the upgrade. It's left to the user to determine which repositories need to be re-enabled, and which might require editing. All these "foreign" repositories have a comment indicating that they've been
disabled on upgrade to yakkety.
You have to
edit each repository entry to determine its status. I'll use one of my own examples.
Here you see that this repository is using an older xenial distribution. I wonder if there's a newer one for yakkety? Copy the URI field to the clipboard, open your web browser, and paste the clipboard into the address bar, and hit
enter to go to the web site.
Here we are at the web site. Click on the
Then we end up here. Notice that this repository does not have a yakkety directory. The newest directory is for xenial. So image #1 is correct, and needs no updating, except for editing the comment field and removing the
disabled on upgrade to yakkety comment. If there was a yakkety directory, we could edit image #1 to show that distribution. Click
OK to save any edits, and enable the checkbox in front of that repository.
Go through all of your repositories like this. Then when you exit
Software & Updates, it'll rescan the newly (re)enabled repositories to make sure that no errors exist. If there are errors, write down the error message, and go back to that repository entry and recheck that the information is correct.