I can think of two ways you might proceed, although you will have to investigate to see if either is possible.
There is a Data Page Declare_CAApplicationSettings which calls a DT called "pyDefault". There is a setting for .WrapUpInFlightWarning = true. You might examine how this logic works (it currently warns if there are any open service intents) and see if you can modify it slightly so that only open intents with errors cause the warning.
Alternatively, you might be able to add some basic FlowAction validation to accomplish the same thing.