To change this go to the MX_GPIO_Init function in main.c, HDMI_HDP and ICE40_CDONE GPIOs share a config section:
/*Configure GPIO pins : HDMI_HPD_Pin ICE40_CDONE_Pin */
GPIO_InitStruct.Pin = HDMI_HPD_Pin|ICE40_CDONE_Pin;
GPIO_InitStruct.Mode = GPIO_MODE_INPUT;
GPIO_InitStruct.Pull = GPIO_NOPULL;
HAL_GPIO_Init(GPIOC, &GPIO_InitStruct);
replace this with the following separate configs for each:
/*Configure GPIO pin : HDMI_HPD_Pin */
GPIO_InitStruct.Pin = HDMI_HPD_Pin;
GPIO_InitStruct.Mode = GPIO_MODE_INPUT;
GPIO_InitStruct.Pull = GPIO_PULLDOWN;
HAL_GPIO_Init(HDMI_HPD_GPIO_Port, &GPIO_InitStruct);
/*Configure GPIO pin : ICE40_CDONE_Pin */
GPIO_InitStruct.Pin = ICE40_CDONE_Pin;
GPIO_InitStruct.Mode = GPIO_MODE_INPUT;
GPIO_InitStruct.Pull = GPIO_NOPULL;
HAL_GPIO_Init(ICE40_CDONE_GPIO_Port, &GPIO_InitStruct);
BTW I just changed the code as accidentally included interupt GPIO settings on CDONE due to copy and paste from my experimental local branch, fixed now!
If this helps let me know, I will change it permanently in the newer firmware I'm working on this week..