Sorry for not getting back earlier. In my tests, increasing the configTIMER_QUEUE_LENGTH did not help. I’m afraid it has to do with concurrency, since I did use the timer API to blink LEDs, which involves a lot of (possibly concurrent) calls to reset the timer, if blinking should keep on.
Before investigating deeper though I wanted to try another way to handle blinking LEDs (PWM, low-power coprocessor) and settled on the latter one. When I have some time, I will try to create an artificial minimal example that resembles my use case – perhaps I can reproduce it again and we can continue taking a look.