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They put their repo first on the list. Packages will default to Fedora’s repo if available. You may specify which version you want, if you both know that it’s happening and know that the package you want in particular is available at both.
I really again do not know how this could possibly be the fault of another repository. Fedora is making decisions for ther distro that circumvent FlatHub, this is not FlatHub’s fault.
That was where it was uploaded first, the takedowns were for it being later hosted on azure cloud services