I think the Dynasty will fall for it honestly, and will not realise their mistake until a decade or so later when they're missing reincarnated souls, but souls are popping up in the empire at a fast pace.

I'm not sure that is how the Beacons work. The Dynasty knows how these beacons work. Due to the amount of time that the Beacons have been out of Dynasty lands I would think that they would expect any souls previously contained in it would have long since been reborn by now. I would think that they would expect to be receiving an empty Beacon (though we don't even know if the number of souls in a beacon is a measurable trait.

Conversely, the recently excavated Beacon is not likely to contain any souls. In the unknown amount of time that the beacon as lain buried it is likely that any souls contained therein have also been reborn. And since the people in the area are unlikely to know the consecution ritual, new souls would not be in it.