So the books (neither O5e or LU) never REALLY specify how multiple reach works. But the fact that monsters exist with attacks with different reaches does suggest such a thing exists (if a monster was defaulted to a single reach, than all of its attacks should have that reach noted, instead of the different reaches we do see on various creature attacks).
So that establishes that a creature can have multiple reaches at one time.
From there, we can just follow the reaction, which says leaves a creature's reach, regardless of which one that might be. Therefore, the answer is yes....you can get a warning strike with either weapon, or both if you have the means of gaining two reactions in a round.
We can actually take this a step further. The rules for Oppurtunity Attacks for example, never says that you have to use a weapon whose reach was left, just that if reach was left, an OA can be taken. Therefore, you could rule that two warning strikes could be done with the whip or moving just 5 feet away, again assuming you have gotten 2 reactions somehow. I feel this is a bit past reasonable, but by the book is allowed. Note that if you do that, it opens up some monster combinations as well (a creature moving back 10 feet away could trigger a dragon's claw OR tail attack with this interpretation, and therefore, would almost certainly use the tail).
