There are no known issues with the HCS plugin or Elite causing issues with it at this time.
The reason why the game state gets out of whack when VA crashes is because the variables we use are not committed to disk until VA is cleanly shutdown. If it crashes then all of them will revert back to the state they were in the last time you closed VA. It's very important that when you restart VA you log out and back into Elite, main menu will do. When you load into the game then important settings, like game state, are passed to the profile. All will be well if you do this.