I feel your pain. I unfortunately had that same problem a lot with my 2014 Model S 60. Having to frequently do the scroll wheel reset was a pain in the neck. I too had my eMMC chip replaced (about 2 years ago). The 'unresponsive screen' started happening about 8 months ago and like yours, got more and more frequent.
So, last month (after kicking the can down the road for over a year), I eventually had to 'bite the bullet' and replace my MCU with MCU2. Since then, I haven't had that issue. The responsiveness and extra features make the upgrade worthwhile.
Total cost was $1,880 USD (that includes the labor), and my service center finished the installation within 4 hours. If you want to keep the FM radio, that's an additional $500, but I decided against that, since I listen to music via BlueTooth on my phone, streaming or my USB drive.
During the 'infotainment upgrade' service call, they install updated firmware, update electrical/data connectors between your car and the MCU2, they give you a new dashboard steering wheel screen (which is higher resolution and DOESN'T LEAK!) and they copy all your information to the new MCU (navigation favorites, user profile data, etc).
So, I highly recommend getting the upgrade. Otherwise, I don't think there is any other way to fix/prevent this issue from persisting.