When I talk with customers new to SCCM there are two things I advise them to not mess with: Heartbeat discovery and the “All Systems” collection.
Heartbeat discovery is configurable, and it is ok to adjust the interval to meet your company needs, but don’t turn it off. It isn’t obvious to the new SCCM admin but there are several maintenance tasks that key off that heartbeat DDR. Disabling heartbeat discovery may cause systems to be deleted from SCCM before you had expected or intended. I don’t ever recommend turning it off.
The All systems collection is a different, but similar issue. That collection has a default object ID of SMS00001. If you delete that collection you can, of course, re-create a collection with the same membership, and the same name. It will, however, not get the same ID. I have seen od behavior when that collection is missing. I have never had the time to investigate the exact problem, but in general I just suggest not deleting it. If you do perhaps delete it then you can restore it. An example is http://blogs.msdn.com/b/vinpa/archive/2010/03/17/how-to-restore-the-all-systems-collection.aspx.
File this under the category “won’t kill ya, but best not to mess with it”.