That's interesting as CZs are semi-persistent (if won they stay that way for some time until they reset and re-logging doesn't reset them - from my experience). If relogging works, in the case you mentioned, this would indicate that the event that spawns the NPC ships can fail and that this can be triggered by relogging. Meaning that the CZ itself isn't reset, but that sometimes certain events in CZs can be re-triggered.
Hopefully this is an indication that FDev might be able to fix that problem quickly.
I wonder if the lack of enemies is down to the CZ having been already won by another player or group. I never stick around after a match as I use ammo heavy loads so I don't know about any timers between matches.