We just tested it with a party, we stood further away and let the Warlock be the only one getting into combat while pulling with the Eye. The Ethereal Beacons that Shaffar has beside him vanished after the Warlock died. The beacons didn't respawn after. We ressed the Warlock and then killed the boss with ease.
Source :
http://wowwiki.wikia.com/wiki/Nexus-Prince_Shaffar
"Note: Bug confirmed. Starting off the battle by sending in an Eye of Kilrogg will cause the initial 3 beacons to disappear altogether. (Tested on 7/19/2008, appears to be fixed) "
We read about this and decided to test if it was bugged or not.
netherspite
commented
6 years ago 
Wednesday Oct 14, 2015 at 00:03 GMT
Originally opened as https://github.com/ccshiro/cc-buglist/issues/1962
We just tested it with a party, we stood further away and let the Warlock be the only one getting into combat while pulling with the Eye. The Ethereal Beacons that Shaffar has beside him vanished after the Warlock died. The beacons didn't respawn after. We ressed the Warlock and then killed the boss with ease.
Source : http://wowwiki.wikia.com/wiki/Nexus-Prince_Shaffar "Note: Bug confirmed. Starting off the battle by sending in an Eye of Kilrogg will cause the initial 3 beacons to disappear altogether. (Tested on 7/19/2008, appears to be fixed) "
We read about this and decided to test if it was bugged or not.