We actually have several examples of disconnected groups based on the same technology:
All of these were based in the same Borg technology, but the main Collective was unable to influence/break/fully reintegrate them without special assistance (and with the sub-collective, it didn't work at all).
In Unimatrix Zero, Part II we also learned that the hive mind allowed for instantaneous galaxy-wide transmission. Axum's ship was on the other side of the galaxy, yet there was no lag when he conversed with Seven.
This results in 2 main possibilities I can think of:
- The two Queens were already in contact due to the hive mind, and command was relegated to the one on site.
- The technology that created the hive mind had changed sufficiently enough in those centuries that the two collectives were incompatible and not (currently) in contact with each other.
- I feel this one to be the most likely due to ENT 2x23, Regeneration, since the drones required sending a subspace message instead of using the hive mind to contact the main Collective.
If they were already in contact with each other, I suspect the two Queen minds would "fuse", sort of creating their own sub-collective. It could act rather similarly to the sub-collective from Survival Instinct - they were part of the whole, but could still separate themselves as a group from the whole.
And if they were not in contact with each other? In VOY 5x02, Drone, the Doctor's mobile emitter is accidentally combined with Borg technology to create a single Borg more advanced than the entire rest of the collective - and the Borg try to assimilate it.
Therefore, if two incompatible Borg Collectives existed, I would expect each one to try and assimilate the other. The more advanced Collective to gain more drones, and the less advanced one to make itself more advanced.