You should check the settings for your FCC agent DCPs. Once the link is back up it should reappear on the topology map after the next time the switch/fabric is discovered by the DCP. If there is no rediscover (or a long delay) this could be causing your issue. I'm pretty sure this is picked up by the Device validation DCP. In my environment I have it running once every hour. If a port dropped right before it ran and came back up right after it ran it could take almost an hour to update the topology map.  On another note, I've been campaigning for a while to have the data on HBA to switch port links made more "resilient". So in this situation you would see that there was a link that was down... and more importantly, when you get an alert for that switch port you could easily tell what was affected.
I'm using ECC 6.1 On a topology map when a FC port on a switch goes down the link between this switch port and a hba vanishes rather than changes its status and appearance and does not reappear when the switch port goes up. Is it possible to force the link to reappear on the map after the switch port goes up?
ECC 6.1 FC link on a topology map