That depends on the SW to a certain extent. It is impossible to remove the connections on the PCB to the HDMI framer. They are connected and always will be. As the HDMI is all inputs, that should not interfere with them being used. As long as there is no HDMI cable plugged in, then the HDMI device should not be active, not that it really matters… It will be up to your SW to re assign these pins for your use.
On the eMMC, there is a reset line that can hold the eMMC reset. That should allow you to use these pins. However, you will have to boot from uSD and not use the eMMC as of course it will be disabled by your SW…TO facilitate this such that you do not need to hold the boot pin, you will need to wipe the eMMC clean. After it boots, you can set the eMMC into reset and reassign your pins.
Gerald