Maybe the 31st Century Starfleet "recruited" his past self. This is similar to what the crew of the 29th Century Relativity crew did with Seven of Nine in VOY: Relativity. Or maybe they retrieved his remains after he was shot and somehow "fixed" him.
Daniels was never killed in the first place, in fact he was never from that time period to begin with. Daniels is a Starfleet Officer from the future trying to stop the Suliban from altering the timeline, this all part of the Starfleet-Sphere Builders War story arc.
Think of crewman Daniels as being chronally displaced all that Silik's attack did was force him back into his own timestream.