Where, oh where did my Dogmeat go?

The pathfinding for NPCs in F3 (and in Bethseda's Skyrim) is sometimes a little dodgy... and to be fair, the terrains in these games can be very complicated, especially around elevation changes.

As a result, the programmers have some "cheats" to get friendly NPCs to logical places (you wouldn't want Dogmeat to reappear in the middle of a hostile bandit camp, for example). You may notice, for example, that in Skyrim you can use dragon powers to sprint/dash FAR ahead of a companion and then turn around to see them impossibly running into frame right behind you.

One of the larger-scale cheats is what you noticed -- Dogmeat disappearing for a looong time and only reappearing when you return to a familiar and safe place.