The app is removed from your "My Work" stream only if publish it the first time.
Selecting the "Replace existing app" while publishing will keep your application still available in your work folder:
You can schedule the app's update through task (even in your Work folder), but I would advise against that.
Manual publishing might be time consuming, but it's safe, IMHO.
Not sure that I understand your issue.
If you do what Vlad said then you don't lose anything.
You make changes in your Work area. Then publish your latest version by replacing the existing app in your stream. The working copy remains in your work area if you want so that you can make more changes. Or get rid of it and the next time you need to make changes duplicate it to your work area and repeat the process.
You really do not want to be updating the published apps directly. Unless you are a gambler.
This process works very well for us. You have to have some controls in place.