Mostly, yes. It will be up to you to replace each instance of SINE with the Kontakt equivalent, but note that there are some minor differences between the two versions. Most notably, the volume of the kontakt instances will be too quiet, so I would recommend increasing the expression (CC11) data in each midi track to compensate. There are also differences with how some instruments react to dynamics and MIDI.
Orchestral Tools - The developer of Metropolis Ark 2 - forbids the distribution of project files that include tracks pre-loaded with their kontakt instruments. We find this unfortunate, but thankfully the SINE version of Metropolis Ark 2 is an improvement and just as enjoyable to use. If possible, we'd recommend updating to the SINE version if you haven't already done so (it's FREE for most previous owners of MA2). 153554b96e