I was able to find a "fix" for this by increasing the projects auto wait timeout to be greater than the applications "non-responsive" load time. What appears to be happening is that the .Find method achieves the autowait timeout and then causes the .Net plugin to fail.
Pseudo code to reproduce:
1. object.Click();
//Long application load that causes the application to become non-responsive
2. object.Find(prop,propVal,depth);
3. autowait timeout is reached (application is still non-responsive)
4. application finishes processing and is now responsive
5. .Find method failed to find the object due to auto wait timeout being less than the applications load time.
6. Extended properties are unavailable until the plugin is reinitialized, Test Complete is restarted, or the test application is restarted.
Hopefully someone else finds this useful, or someone at SmartBear can reproduce the issue and get this fixed in a future update :).