The following is an excerpt from page 15 of the Warhammer Annual 2002 release with an expanded explanation by Gav Thorpe regarding the Order of Combat Resolution.

One source of contention that has been brought to my attention is the order in which you should calculate combat results and make subsequent Break tests. This is because Generals and Battle Standards can break and flee, which could mean that nearby friendly troops would not be able to use their special rules. Personally, I always treat Combat Resolution as simultaneous, so that if a unit was within range of a General or Battle Standard after all combats were fought (but before troops break and flee) then they use the associated benefits. By the same token, rallying is worked out the same way, so you can't test to rally your General first and then allow nearby units to use his Leadership to rally in the same turn.

The same applies to breaking and pursuits, and my advice would be to make any fleeing and pursuit movements in the order that makes it the most physically convenient. The diagrams below show what I mean by this.

Sometimes a pursuing unit will crash into an enemy unit fleeing from another combat. In this case, the enemy unit isn't wiped out as it hasn't been caught by the pursuing foe. In this situation, all normal rules apply. Firstly, the pursuing unit counts as charging. Secondly, a unit that is already fleeing when charged will automatically flee again. So if a pursuing unit moves into a fleeing unit, the unit will make another flee move and will either get away or be wiped out if it can't outdistance its foe.