If you commit the AppStore module immediately after downloading it, you can easily use the Show History option on such a module (right click on module --> show history). You can now see which microflows have been changed. This enables you to export these microflow to import them again when you have updated the module. Any domain model changes will be still be lost though.
You could copy the microflow to your own module, and change that one, in that case, when you download a newer version, it won't get overwritten.
Usually modules have a DOCS / README / USEme folder, with a version in it. You could compare that to the latest appstore version, however, not every module updates the version number in the module...
I am working on a similar problem, I noticed how some associations were completly gone after updating the email module. To compare old versus new I just moved the old DM Entities (and some pages) to a newly created TEMP module. This way I maintain the previous changes and data. I guess you could try if this helps you as well.
In addition you could create an export of your old module before updating.
Edit: note that I intend to copy the entities back from TEMP back to the updated Email module in my case to maintain previous associations, otherwise this would not be best practice.