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Just for background, I have a subsystem (let's call it subsys.qsys) which contains my HPS block and some peripherals, one of them being a clock_bridge component. This bridge brings the mm_bridge_0_clk port from the HPS up to the next level.
In my main system (lets call it sys.qsys) I bring in the subsystem and I distribute that bridged clock output to more peripherals and some custom IP, including another clock_bridge to further bring that clock up to the top level project .v file.
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Not really sure if this relates to the warning you see https://www.intel.com/content/altera-www/global/en_us/index/support/support-resources/knowledge-base/solutions/rd11172011_691.html

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