I have noticed that it appears to not be occurring as frequently since I split up the identification tasks. I created one group for the servers and another group for the chassis components (OA, iLO's, etc.), with them running about 4 hours apart and I haven't lost any associations...unless the iLO was actually not responding. This is with HP SIM 7.3, latest patches and SQL express. It would be interesting to know if people affected by this issue are running a full SQL version or the express edition that's included with HP SIM.
Also, when I have lost associations, usually re-running the discovery task with just the OA IP brings everything back into order...I have not had to delete any systems in order for them to be associated properly.