The assention missions are unfortunately not retroactive, so they will not take into account any previous work you did on champions, you will have to plan accordingly for the next ones as well. I have been there and it can be frustrating, but if you plan them out you should have no issues :) 

Ah I see, is there any other missions past this point that I would have to worry about as well? As in non-champion missions? I do know the Guild Hall is another one but not sure if Part 3 & 4 will have any of these types of missions that wont count if you've done it already. Also thank you Rufus Shinra for the warning for future champion missions, luckily I had a champion that was worth being a 5-star, so no wasted materials. ^^

As far as I can remember the champion ascention ones are the only ones to watch out for, all the others are retroactive, but some can be challenging/resource consuming , for example crafting 10 potions of each affinity , autoing stage 20 of all dungeons, clan boss damage, however hopefully you'll have developped your account well enough by then. 

Good luck !