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There's a lot of similar questions:

This is most commonly an issue with network connectivity.

You're having issues with the new url so it's not related to the recent update to rosdep for the github url change.

You should validate that you can get to that url by default.

As for the upgrade yes, you cannot keep the same ROS version installed between 16.04 and 18.04 as they are not both supported by a single ROS distro. See here for target platforms: