Trying to help but you need to be much more specific; to be clear, do you mean that you flashed one of the pre-baked QMK hex files from Ellipse, or do you mean you created a custom layout using the web-based QMK Configurator?
Having a split backspace with the left 1U being Backspace and the right 1U being Del is fairly unique so I'm guessing you went to the web configurator and created a custom hex file?
The reason I ask is because yours sounds like a software issue: a key with threshold of 0 is treated as a "dead" key, and the capacitive-sense auto-calibration routine will skip over a key and set it to threshold 0 if that key is not mapped to any function on layer 0. So it would be helpful if you took us step-by-step through exactly what firmware file you are flashing, and if it is a custom-generated one, be very specific about the steps that you went through in order to configure it. Perhaps it would even be easiest/best if you simply screenshotted what the QMK Configurator looked like immediately prior to you clicking the "Compile" button (so we can see what the "Keyboard" and "Layout" drop-downs have in them, as well as what particular function every single key on layer 0 is mapped to).
If you mean that your keyboard is physically configured for split-backspace (has springs & flippers in both barrels) but that you are flashing a QMK hex that is configured for a non-split 2U backspace, and you assumed that pressing either key would result in Backspace being transmitted...that will not work. You need to actually assign real key functions to both keys for both of them to work. You can set both keys to duplicate functions (e.g. Backspace) if you wish, but they must be set to something, not left as "N/A" (QMK keycode constant 'KC_NO').