Hi @Norick
On the other side you changed the origin design and cut off the clock control block (see orign file at the top again). Of course without clock control block the warning dissapear but again it is a different design.
==> Yes, that's what im trying to say. It is the clock control block that is causing the problem. Thus, my recommendation is to instantiate as "B" (not A), you shouldnt have a CLKCTRL block in between. The CLKCTRL routes to a clock network, e.g. GCLK before going to the PLL. Thus the warning.
If you want to avoid the warning, connect the dedicated input clk pin directly to PLL (without CLKCTRL in between).