I was able to repro this, and have entered it as UE-53777. From what I’ve been able to determine, stopping the test framework in the middle of a long-running latent command blocks the save functionality. Until this is fixed, you should be able to mitigate this be restructuring your tests to return as soon as the behavior under test can be verified instead of relying on extremely long waits.
I strongly recommend against editing the automation test macros. If you need behavior that the macros don’t provide, it would be better to create a custom subclass of FAutomationTestBase instead (see FClientFunctionalTestingMaps in ClientFuncTestPerforming.cpp as an example).