Deleting files in here does nothing, well, other than clean it up and possibly free disk space. Please do not get confused with cleaning this folder and troubleshooting problems. These files are purely historical. Deleting them is like trying to fix a problem by deleting the log files. It wont work.
There are a few things probably that happened here all in concert.
1) when we do an AD import and/or network discovery, and computer discovered that is NOT managed will become a predefined computer. Known issue. I've actually been just talking with Dev about this issue today. We don't have an excellent work-around for that issue, which is why I'm pushing on it.
2) IF you had respond to predefined computers checked, then it would do what you described.
3) SBS server service (which responds to PXE boot requests) doesn't ever "forget" something, but has to be updated by an actual request from the SMP. IF it is told to respond one way to a computer, it will keep responding that way until told otherwise. OR until it's restarted. This becomes important for instance when you delete a computer in the console. The SBS server service doesn't just "forget" about that computer and stop managing it, so you have to restart the SBS server service to get it to ask for a new list of computers which will not, at that point, contain the deleted computer.
4) It is a known issue that sometimes the SBS server service will treat "known" computers or managed computers as "unknown" because we only send, by default, a list of known computers to the SBS server that reside in the same subnet as the SBS server. We have a KB that discusses how to modify the query that sends this result to include all computers assigned to the task server, OR include all computers in the environment.
Again, do NOT concern yourself with deleting those historical files. You can of course at any time do so - it makes no difference to us, but it wont solve any problems at all.
Finally, please visit http://www.symantec.com/docs/HOWTO55859 for more information on how to get around some of these issues. That's an excellent KB to bookmark.