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I had a similar issue a few years ago when I purchased a kepub only book. Like you I never sync to get books I always side load the epub through Calibre.
It took a few days for kobo to understand what my problem was (they kept telling me I didn't need an epub and gave me instructions on how to sync about a hundred times!!) but eventually they did offer to refund my purchase.
However as I was about to accept the refund they then decided that it was a mistake that the epub was missing and suddenly it appeared on the website for me to download.
I hope you are able to get a satisfactory solution.
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