One daily roll
(Combining navigation, hazard, and encounter.)
Make a nav check. DC 12 for clear skies (±5 for fast or slow pace).
On a nat 1 there’s a hazard (GoS p200). On a nat 2 or nat 3, there’s an encounter (GoS p207). (These special die values are instead of being lost.)
Either way, make a new nav check after surviving the hazard or encounter. However, there can’t be two hazards or two encounters in the same day. So if you rerolled after rolling a 2 and then roll another 2, then just treat that roll as a normal 2 on the nav check.
If there is a hazard followed by an encounter or vice versa, make a third nav check, treating 1, 2 or 3 as normal.
Finally, if you do end up lost and want to find your way back, the base DC for that (for “pure” nav checks) is 10 instead of 12 and 1, 2 and 3 are not special.
Fishing and repair rolls are still separate daily rolls.
Advantage / Disadvantage
If you have advantage, which you do as long as you have a map of the region, one of the dice need to have a special color. The “hazard die”. The other die is the “ordinary die”.
The group can decide what works best: rerolling the ordinary time every time, or letting it sit while just rerolling the hazard die. That doesn’t affect the probability as long as you stick to one of those two methods.