In this particular design D1 is a “protection” diode. It prevents anything from happening if the battery is installed backwards since electricity will only flow through it in one direction. The MCU and voltage divider are both powered by the output of D1, which is slightly lower than actual battery voltage (say around 0.25v lower). In the future the schematic will very likely look slightly different. Take a look at the most recent discussion in Tom E’s BLF17DD Info Thread - Reference thread for more info.
As it stands with your driver you can stand to lose the entire trace all the way up to the via - just solder D1 from the top of R1 over to the BAT+ pad. Like you said though, you’ve got the problem solved and there’s no big reason to continue to mess with it. Maybe add a little glue if you’re not confident. I understand that it used to be common to glue IC’s onto PCBs.