ESP32 doesn't wake-up from deep sleep when battery goes flat

[simonccnomis]

We have battery powered ESP32.

In the program start, a custom button is configured as an external wake-up source (through RTC GPIO). Afterwards, once application is done, device goes to deep sleep. Normally, I am able to wake-up the device with the button afterwards.

I only encounter problem in following scenario:

leave the device active for long time, battery discharges.
charge the battery so that device can get enough power.
press the custom button to wake the system - nothing happens at all.
reset the board - the system works normally again. Button for waking from sleep works.
So, the issue is that after some time device forgets that it can be awaken with the RTC GPIO. Only way to restore it is with manual reset.
Any idea to correct this?