Encounters missed/avoided were either planned via map-key, alluded to (as per my example upthread), or avoided by tactic, missed via timing etc.
I missed your birthday party, I missed your dad's funeral, I missed my aeroplane, I missed my doctor's appointment. This is all common parlance and those are all encounters.
i.e. the DM planned several encounters in the fortress but the PCs tactics ensured they avoided/missed/bypassed them all by using Teleport to find their way straight to the dungeons to rescue their comrade.
Because of the nature of how D&D works, especially combat, I will typically have ideas for the path I expect the players to take and then sketch out 2-3 additional encounters that kind of make sense for the location they will be in. I don't direct the players in a specific direction, but I do expect that if their goal is to stop the Mad Mage of Grimston that there will likely be a confrontation with said mad mage.
Most of my notes are on factions, what I think will be important factions and NPCs (sometimes just links to other details). My combat encounter planning is frequently pretty bare bones, a sentence or two along with a list of creatures and numbers. As an example, they were searching some ruins for a McGuffin and while I didn't have a detailed map I knew there were several possible encounters depending on approach. There was another group searching for a different McGuffin (hints at a possible future thread they may choose to pursue). Depending on approach, time of day, how stealthy they were trying to be, they may or may not directly interact with this group and even then there was no guarantee of a fight.
So my encounter notes are pretty bare bones.
Looters - they're looking for the Amulet of the Death Lord rumored to be here.
Mage CR 6
Tough Boss CR 4 x3 (5,600) x4 (6,700)
I had a quick note about what faction the looters are associated with and either 3 or 4 toughs based purely on game considerations. It was up to the players how they approached this group if they did encounter them, the looters had reason to be wary of them but not necessarily hostile. As it turned out the characters decided to attack after just finishing up fight against some vampire spawn without recovering and ended up having to surrender. Which then led to some improv and them bribing some hired mercenaries with a promise of reward followed by an encounter I had labeled "Don't go into the woods at night."
The fight and ultimate escape were just another change in the direction of the session that I never would have predicted, but that's why I find sandbox games fun. Just like in my session with the characters trying to stop the hags where they bypassed an encounter I had anticipated would probably happen because the player's choices drive the fiction forward.