In Vivado 2016.3, I see the following ERROR messages when I try to save the constraints after making some changes in open implemented design. I am saving by selecting File --> Save Constraints or using <Ctrl+S> and then selecting to update current constraint set with no existing XDC file in project.
I see the following commands in the log file:
Also, after running these commands, the generated XDC is empty, which then makes the project out-of-date.
Using the same flow in Vivado 2016.2 works fine and the new XDC is created with updated user constraints.
This issue should only occur if there is not a constraint file in the constraint set before the implemented design is opened.
In order to save changes that have been made, a user will need to create a new constraint set (Save Constraints as) and save constraints to the new constraint set.
This issue is scheduled to be fixed in Vivado 2017.1.