On an ESP32 millis() is just a function. An ESP32 uses several cycle timers, one cycle timer is a micros timer instead of a millis() timer. If you have hardware timers setup on the ESP32 they are completely separate from the cycle timers.
Code snippets are hard to troubleshoot. Yea, I know 100000 of millions of lines of code your project is. Only you know your codes interactions.