Being a stone mason I have worked with lots of limestone and it is subject to breaking at times.
While it is strong it can also be extremely weak and has holes and fissures.
The article states that 2 km disappeared (in the middle or so)from this river, so it didn't dry up and the whole river isn't gone.
Water seeks the lowest point and will go through very small places.

This could be tectonic movement which caused a crack to open up enough to allow this or just erosion which finally broke through.

Maybe OP, could you find the map coordinates and the location of the missing section like an aerial shot and this would show quite a bit.