As described in the title of this article, the issue the user is facing is that Flow Action inputs are being lost when moving a Flow which is a part of a custom application from instance 'A' to instance 'B'. The user wanted to know why this is happening.
A Problem (PRB) was logged to document this behavior as it existed in Madrid: PRB1371306.
The Product Owners reviewed the affected behavior and, after carefully considering the details therein, concluded that this behavior was fixed as a part of an enhancement in New York.
As such, there is no workaround/backport that will be done for Madrid for this issue.
Therefore, it was recommended to the user, to find relief from the behavior, to upgrade to New York where the behavior is fixed.