I was able to prevent the auto-reset by disabling thermal_zone0 on the board. got the idea from: https://forum.pine64.org/showthread.php?tid=6276&pid=45169#pid45169
After setting the mode to 'disabled', the pwm1 does not get reset anymore. Note that the next reboot will reset the value to 'enabled'. To make it permanent, I added a udev rule as suggested here: https://forum.manjaro.org/t/persisting-change-to-sys-class-thermal-thermal-zone-mode/53556
The rule in the post didn't work for me however and I went with:
KERNEL=="thermal_zone0", SUBSYSTEM=="thermal", ATTR{mode}="disabled"