The size of content repository folder in the SEPM (SEPM\inetpub\content) is one of the biggest concerns for SEP administrators; when the partition which hosts it is almost full, they often manually delete the definitions to free some space without knowing they are damaging the installation (broken links, no deltas for SEP clients, etc.).
It would be nice to put there a README.TXT there where it is written something like:
Do NOT delete any file here!
If you have disk space issues, follow this article:
http://www.symantec.com/docs/TECH96214
or call the Technical Support.
Maybe this will reduce the amount of incidents caused by tampering that folder.