Do you have any smart devices like bulbs or something that get physically powered down (mains cut off with a dumb switch, for instance) at night.
If so this will mess your mesh up big time.
Also do you have enough routing nodes in your mesh?
Here’s some reading on setting up a mesh for zigbee.
https://community.home-assistant.io/t/the-home-assistant-cookbook-index/707144#p-2856943-zigbee-21