The very first page of Chapter 3 (p.38) states
"...water travel makes it difficult for their drow pursuers to track
and then later (on p.44), we read
"Travel along the waterways of the Darklarke is and excellent way to
throw off their drow pursuers (see chapter 2 for details)"
...so I think that's all the evidence we need that the drow DO, in fact, continue to track them and that you are supposed to use the rules from chapter 2.
So the question then becomes, how does being on the Darklake affect the base pursuit rules from Chapter 2 p.24? I would say that they don't change at all.
"decrease the pursuit level by 1 for each time the characters cross or
traverse some feature that obscures their trail, such as a
...so that's going to be every day they are on the Darklake, and that's why its an excellent way to throw off pursuers. All other things being equal, you are reducing your pursuit level by at least 1 each day.
None of the random terrain encounters from chapter 3 provide the kind of pursuit modification you find in their chapter 2 counterparts, but that's because they all involve crossing water in one way or another so you just apply the 1 point reduction as stated above.
Of course the other factors that raise or lower pursuit level are still in play, such as
"increase the pursuit level by 1 each time the party has a random
encounter with one or more creatures, unless the encounter is bypassed
or avoided completely."
Traveling at a fast or slow pace is going to be relative on the Darklake. We know that drow lack a swimming speed so they are stuck paddling just like the PCs.
I would lower the pursuit level by one for any days that the party is doing forced march rowing (more than 8 hours) and I would raise it by one each day that the party just drifts along with the current such as in a makeshift raft.
I would not allow any party members to make the "covering tracks" checks, since there aren't going to be any tracks in the water.