Create a flow such that it has a multi output decision box ( outputs Item A, item B , item C)
Add a subflow in the main flow such which also has a multi output decision box ( outputs Item D, item E , item F)
Now once the model is stitched onto main flow, add constraints in a way that item A should not appear with item D.
Save the model
Close it..
Open it again.

Resulting Output:
The constraint saved in above step is not there and it removes all other constraints attached with subflow.

Coding Error.

ARD Version 2.11.000.5

Fixed the constraint's problem and have successfully tested the following build 2.11.000.12  Please contact BC Support for this version or later.  If downloading a GA version after February 19, 2019, please contact BC Support and verify that this fix made it the latest GA.

Video URL on how to open a Support Case - https://communities.ca.com/videos/5898-demo-how-to-open-a-support-case
You can download the latest version of ARD by following the directions in this document: https://comm.support.ca.com/kb/How-to-Download-Agile-Requirements-Designer/KB000009613
To contact support, go to https://www.ca.com/us/services-support/ca-support/contact-support.html.