Reading the iCloud design docs, it mentions:
Because the system tracks changes to the document, it is able to
upload only the parts that changed, as shown in step 2. This
optimization reduces iCloud network traffic and also reduces the
amount of power consumed by the device—important for battery-based
devices.
In my scenario, I have a plist file that a UIDocument tracks. What if I replace the plist file with a copy of same plist, same filename, same path? I know that the metadata gets updated, but does the entire file get transferred over to iCloud again?
iCloud does not track based on UID, it tracks on filename. Your file will be diffed and only the changes will be sent to iCloud.
If you want UID tracking, Apple recommends that you add a UID and document schema version to your file formats (as they do).