There are certain bosses that, due to the nature of the instance they're in, can't be repeated. It's not because the instances are a one-time entrance. Usually it's because they only spawn when someone has the quest to defeat them. Here's my list of ways to fix this.
Chester Droors: Since the duel circle doesn't exist (or at least is inaccessible) in the pre-quest version of the classroom, just make it so he always spawns. Blackblade: Have the orbs in his instance be intractable regardless of whether the player had the quest. Senator Nellek: Have him stand outside his cave until the quest gets to the part where you fight him. Morn Shadowbrew: Have her come outside the house after being defeated. Queen Tanei Ghostmane: Have her come outside the cave after being defeated. Igoka Defender/Painted Greyhorn: move the fight with the Igoka Defenders to a separate instance in the hut across the road. I suggest calling it "training hut". Shaka Zebu: Have the first visit to his throne room be a seperate instance accessed through the door behind Amahle Autumnrain. (the existing instance already has a matching door in the back corner.)
Have the Calendar Stone appear outside, possibly in the nook between statues behind Tezcat Threestar the Zocalo, so that there's no need to re-enter the Pyramid of White Fire.
In my opinion they should just take another look at monstrodome. It obviously flopped and after all that farming, being able to return to the boss directly for drops wouldn't hurt anyone. Spell giving bosses being the exception.