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I fixed my issue!
I ended up factory resetting, reverting to previous kobo firmware, and reinstalling Koreader.
I think the problem with the tags not showing up was due to the kobo firmware being too high, so calibre couldn't modify the collections (I think? Not too sure). The problem with the books not showing up in the series was because the device wasn't refreshing after every time I uploaded a new book, thus when I played around with the metadata and thus folder structure, files were moved around / deleted, but since the metadata wasn't being updated they weren't being shown when I searched by metadata.
Now my main problem was why wasn't the kobo updating and refreshing when I uploaded new books via calibre? I'll post that question in the proper forum when it comes to it. For now this thread is officially solved. Is there a way I can mark this thread as solved or something? I'm not used to this forum format
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