This keeps happening to me and when it does I seem to have to "flatten" all settings, reapply firmware to be able to get things working again.
I set up a coordinator and a router set to AP  and when I scan the radio network both of them show up and are connected.
I then go through the process of changing them over to micropython and add code so that they talk to each other, still fine and connecting to each other.
This is where I think something is going wrong. I change the sleep mode or the router to Micropython Sleep  and edit my code so that it does go to sleep and wake on a contact closure but then it will not connect to the coordinator when it wakes up.
From this point on, if I change the sleep mode and the AP back to  then in XCTU I get
Error discovering neighbors of <mac>
Cannot find the local device of <mac> address.
Remove it from the Radio Modules list on the left and add it again.
That doesn't resolve anything and I have to go down the route of "flattening" it again.
Is there something that I am missing with regards to activating MicroPython Sleep?
It's not that it isn't waking up again, it is. And even if it was, if I change that mode back and AP to API mode then this should stop it from sleeping.
I'm about to start again to try and pinpoint the exact moment that it breaks but any ideas as to what is happening would be welcomed.