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Did the Triarch Praetorians retain their Free Will, even after Biotransference?
It seems like they did, as the did choose to protect the Tomb Worlds for 60 Million years instead of going to sleep like the other Necrons

They probably have a degree of free will on par with Lords and Crypteks.

Triarch praetorians certainly retained more personality than common soldiers, but like all necrons, they were controlled by command protocols during the war in heaven (at that time, no necrons had free will besides the silent King). After the necrons went to sleep, the silent King removed all of the command protocols. The Triarch praetorians stayed awake to try and spread Necron culture, and their ability to do so makes me think they were given a level of personality superior to even lychguard (probably close or equal to that of the lords and crypteks who they have to keep in line).

Considering the independent nature of the Praetorians' assignments, I would think that they would retain a large measure of free will.