See designer's page...
Frohes neues Jahr!
Miquel is pretty much on target:
Q1: How do you combine the two fleet parts? or did they become separated?
They will become two separate fleets, in different sea zones. Assign a new fleet marker to one of them. If out of fleet markers, give one of them a temporary one and assign it an abort mission.
Q2: In 5.2 Missions the following is said about raiding fleets: "... a player may assign a raiding mission to no more than one fleet, which must include a leader and may contain no more than two ships (not counters). Limited to warships and colliers."
If I read it correct only two ships are allowed in a raiding fleet?
5.24 says that you may divide a fleet during the Orders phase, including fleets with Raid missions.
How is that possible with a raiding fleet? In 5.2 it is said that only one raiding fleet is permitted. And if you divide a raiding fleet, both fleets only have one ship.... And what about the leader?
The default for Raiding fleets is per 5.2: no more than one fleet, with a leader, and at most two ships. Unless the special rules in a scenario say otherwise (more than one Raiding fleet, don't need leaders in Raiding fleets, can have more than two ships in a Raiding fleet), you must abide by the 5.2 restrictions.
So if you have to divide a Raiding fleet due to separation per Q1, give the one without the leader an abort mission.