Electrical – 12/3 to disconnect box for mini split install

Since you have a 2" PVC (assuming schedule 80) conduit here, providing 742 mm2 of room for wire fill, and your 3 2AWG wires (assuming THHN/THWN or XHHW here) only take up 66*3 = 198 mm2 of that space, you have plenty of room to stuff a bare wire down the conduit to bond the subpanel and main panel grounding bars together. A 6AWG bare copper wire will do the job, and should be fishable through the conduit with the power to the main panel turned off. Connect it to the ground bar in the main and sub panels, turn the main panel back on, and you're in business. (Of course, if you don't want to play "fishtape wrestler" for a day, you can pay the nearest friendly electrician for that service instead.)

P.S. no, you do not need to remove the ground rod once you install the bonding wire between the two buildings -- in fact, current Code requires outbuildings to have their own earth ground, in addition to the bond back to the main panel's ground. (This is done to keep all the wires to the outbuilding from soaring to some crazy-high voltage in case lightning strikes near the circuit conductors.)

If the two circuits are wired with 14-2, all you need to do is identify which neutral goes with which circuit and disconnect them from each other, so each is only connected to the items on its circuit.

This would only be a problem if the two circuits were actually sharing a neutral wire. If they simply have joined neutrals, it's easy to remedy.