Now I question if I should just restart and rescan the amiibos again after the opening cutscene... I think I might do that.
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Sorry for the double post but as of right now my intentions for sharing my saves will be All amiibos after opening cutscene (JP and US) and 100% on absolutely everything (JP and US). This is mainly because if I tried to share my save for something specific I may of already passed that point already. My Amiiqo is set up so it goes in order of how the folder I got from that ISO site is set up in terms of series and their amiibos. To completely re order the bank would take eternity so I just put what I need in front and fix the order. For me to scan all the amiibos could take a total of 1-2 hours given how many their are. So if I can help it I'd prefer to have to only do as many times as is absolutely necessary.
There is one problem though. As things stand right now it's a complete nightmare trying to unlock my Amiiqo using my phone and so to compensate I have ordered a USB reader yesterday which should arrive in 3-5 days. So what I'm saying is, I plan on doing this shared save over but it might take time to do right. Also I don't think it's gonna matter which save slot I do this on since I'm pretty sure there's ways to manipulate JKSM into reading the save as one from another save slot.