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The way to go is uninstalling libjack via rpm -e with --nodeps and possibly --force options and then install libjack2 immediately after. That will shut up the complaints from installed jack apps. OTOH, having more than one version of libjack lying around (eg. one under /usr and the other under /usr/local) is prone to a plenty of nasty problems, the least of it is having a broken jack ecosystem. Make yourself a favor and don't.

Cheers