Hi, Martin
In your application, you would like to set GPIO and LPTMR as two LLWU to wake up MCU from LLS mode. Yes, as you concerned, there will be a missing risk in your operation. As you know, NVIC is disable in LLS mode, so one of these two LLWU will really wake up and other interrupt will lost.
I would like to give you a suggestion. I think your concern is pin falling edge is missed. I think you need to check the pin level when MCU wakeup from LLS.
Our LLS wake up timing about 5us. So I think the low level of pin will keep after MCU wake up from LLS.
If your pin pluse is shorter than 5us, sorry, it really has missing risk.
Hope my reply can help you.
Best Regards
Paul