After talking with Tarik, it seems our approach to FPGA/HPS communication was a bit off.
We wanted to use one data bus for writing on the LED band controllers and use GPIOs for the other signals coming from the HPS. It turns out that the GPIOs of the HPS cannot be directly connected to the FPGA, and according to Tarik the workaround are a bit sloppy.
So instead we decided to use the second data bus to write on registers in the FPGA, which will create the needed signals. The first bus will stay dedicated to the DMA module which transfers RAM data to the LED band controllers.
To generate those signals I created an avalon slave (hps IO) on which the HPS can write. Thanks to Romain, the FC setter modules are now avalon slaves as well, meaning that the FC value can be set for each LED band by the HPS.