Miraak can't suck all the souls you've already used, can he? After all, they are bound at this point. I have probably 20 extra at this point and have about 10 shouts (4 are complete all three levels). Is Bend Will in that temple?
I also find it fun to go back and kill the dragon again at a site I've already done, if for no other reason than I'm a greedy pig and want more bones, scales and moola!
No he does not ! At least it never happened to me. I have played Dragonborn 3 times already and he never deleted or stole any dragon soul I was keeping in my inventory. What he does is, that he does not let you suck a dragon soul between when you get into his temple and when you cleanse all the shrines. Once all of them are cleansed, you are able to continue sucking any dragon soul. Apparently, the shrines are corrupted by him and while they are, he has full control in Solstheim over everything that is going on in there; when you finish with that quest of temple of Miraak, you are following this lady to the Skaal village and the boss of that village ask you two things : to get the first Bend Will word and after that, using that word on every single shrine, to clean them out from Miraak’s corruption. Once all of them are cleansed, then Solstheim is back to normal and Miraak loose control over the dragon sould matter.
But to be sure you are not relying on that, I suggest to show up in this island with at least 6 - 9 dragon souls. Reason ? First one you will unlock will be Dragon Aspect and then Bend Will. But it is critical that you show up with at least 3 of them to full unlock Bend Will otherwise, you will not be able to continue. If you show up with only 3, then do not use any to unlock any shout but Bend Will. Anyway, you will not need any other shout to face Miraak but Bend Will and the other shouts you get in this island, can be unlocked once you kill him.
Keep in mind that right after Miraak is finished by Mora, you will automatically suck about 7 dragon souls from Miraak’s dead body and you can use those souls to reset you skill trees right there in Apocrypha. Remember that if you do so, you must spend one soul per each skill tree you do reset or you can use your souls to unlock the other shouts and come back there to reset your skill tree anytime you want later in the game. Happy gaming bro.