Not true. You can run TWS using TWSStart (from the IB TWS group) and start it at noon Sunday (Eastern US time) and have it stay open until midnight Friday night. Without closing once. TWSStart will intercept the auto-logoff dialog and automatically change the time to an earlier time to avoid logging you out.
A few years ago IB customer service explained that the auto-logoff was a security feature/requirement. I recently requested that the "feature" be changed as IB now has the "Security Token" system up and running and we are probably very safe. If you'd like this feature to go away (or made more reasonable) go here: http://www.interactivebrokers.com/en/general/poll/poll.php?ib_entity=llc Search for suggestions by contributor "JackR" and you'll see my idea. Vote - now and on November 4th. Jack
Your system is not very robust by sounds of things, it should be able to handle TWS shutting down, even the PC/server going down for some unknown reason and recover properly. You can get TWS to tell you about your open positions and so you should be able resync your ATS. I also use a transactional database with my ATS rather than keep everything in process memory.
You are making assumptions. The system does include heartbeat monitoring should the network timeout. The issue was that TWS was closing altogether and I did not know why (well I do now). TWSStart does a good job of flipping the PM/AM timeout to prevent auto-exit. I do like the database idea though. I will look to implementing that.