After killing Runhorn and the Dark Portal...
 

I've just killed Runhorn and closed the Dark Portal but left some armies behind that I did not defeat, can I come back later and kill them? And all my troops are gone I had when my fight with Runhorn was won. They gone forever? Can I go back to the 4 islands?

Of course you can, you just need to finish certain quest first. Note: You can distant travel by boat only from Greenwort later on, not from Arlania or Wastes.

And my missing units?
 

Ty but what about my missing units?

gone :)

Yep, gone. No too much harm done though, except if you had any maidens in your army because these tend to be quite rare. All other units are available in large quantities though.

Word of warning - don't leave any valuable units (dragons, paladins) in the castles on the main continent either ;)