That one's tricky. Some GM's can do it really well (I played with one fellow who GMed PCs so well when their player was away, that we gradually forgot which actions had been initiated by the player and which by the GM); I don't think I could.
I *do* think that making sure that the "camera" follows only the (present) PCs, and using a few time tricks (e.g. fast forwarding through that one day where missing PC X's actions are truly vital) should work, if carefully done. I think that's what I would do. I don't know if there's a general tool or principle that can be distilled from that kind of technique, though.
It probably depends a lot on the game in question, right? Like: How closely tied are the PCs? (e.g. Is it a large holding, with hundreds of NPCs, or three brothers traveling together in a minivan?) Do in-game reasons for absences exist, like weird blackouts, or constant trips out of the holding to gather water two days away, for which people from the holding are chosen by lottery?
If you're starting a game from scratch, you might be able to get some good ideas on this stuff from the players. "Does your character ever just disappear without explanation, or have duties outside the holding, off-screen relationships, etc? What's that like, how often does it happen, what does it mean to you?"