Symptoms
After cloning/syncing example.com to example.net under Domains > example.com > Clone/Sync, the encoded strings are not updated.
They are kept as https%3A%2F%2example.com in the destination database, while should be https%3A%2F%2F2cloneexample.net.
Cause
WP Toolkit bug EXTWPTOOLK-1789 fixed in WP Toolkit 3.6.0 on February 21nd, 2019.
Resolution