The acronym AFK is short for "away from keyboard" - meaning a player who is still in the mission but temporarily not playing. Players who are AFK are not treated the same as players who have been killed, since they are liable to come back at any moment and resume playing. They do not automatically lose their position in the chain of command, though they may assign someone else from their unit to handle their role temporarily.
In general, players are discouraged from going AFK unless it is absolutely necessary (e.g. a "real life" emergency). Other players will not normally wait for an AFK player to come back if they've been gone for some time. If the player does not promptly return, they may be declared "effectively dead" and their role inherited by the next person on the chain of command. If the unit is given orders to move (or is already moving), an AFK player may be left behind - even in a location where they are likely to be killed.
Once the player returns, they are expected to announce that they are no longer AFK.