This is usually due to a scan running at the time of the update.
When a scan is running on a machine, it will lock the currently loaded definition on the machine. In the mean while if a new definition is downloaded by the SEP client, the old definition will be marked for deletion during reboot (as it is currently being locked).
This issue was identified on SEP clients running 12.1 RU1 MP1 or earlier. But it is not necessary that this will happen on all these clients. This was fixed in SEP 12.1 RU2.
Old definitions require a reboot in order to be removed
Fix ID: 2692127
Symptom: Old definitions appear to require a reboot in order to be removed. This is usually due to a scan running at the time of the update.
Solution: Updated the Common Client component to resolve a condition where the scanner held the virus definitions open, which prevented an update.