The Six Sages died in their respective temples in Ocarina of Time. (Theory)

[ninjadynamo]

i assumed they died sometime during the war while u were trapped in the temple of time. like ganondorf rushed into kokiri forest and slayed everyone, and saria was likely chilling in the lost woods and was like trying to protect it when she died.

They couldn't have died then or after. If they did they wouldn't be sages. Rauru is the last living sage after Ganondorf's take over, he sets Link to awaken the new Sages which are who we meet in OoT. If they died then they wouldn't have become sages. Sages can die and death is not an initiation to being a sage. If that were true in the series lore then Wind Waker wouldn't have needed sages replaced nor would Ganondorf have been able to kill the Sage or Water in Twilight Princess, especially if the Sage was already dead.

The sages are alive and couldn't have died.