Navi notes

Navi appears 30 seconds after entering an area, then disappears after another 2:00 have passed. So you have a total of 2:30 in a area before you lose navi. The navi timer does not count up when you are in text boxes, door transitions, cutscenes, pressing ocarina in the air, etc.

The timer gets set to 0 when you enter a new area, die, or savewarp.

If you use or lose navi (the timer gets past 2:30 in an area), then the timer will no longer get set to 0 when you enter a new area and you will have to wait 19 more minutes for the timer to wrap around to 0 again, letting you get navi again (after 30 more seconds). Those 19 minutes can be spread across multiple areas.