It would be nice if instead of the conquest currency you could use crystals to unequip. This would allow people to save the currency for character shards and maybe give a bit more incentive to swap disks around. It would also prevent what happened to OP.
Other than that you could always plan out disks a bit more. Before you start check out all bosses (you can see them) SLKR was obvious you dont want to have tm removal disks because tm removal stacks health. I am in sector 4 still and while I have picked up some of the decay TM disks I am waiting to equip them until after I beat the SLKR boss and then go back to try some of the tm removal feats.
