Sensor readings inbetween Deep Sleep using RTCZero library [SAMD21]

[Phec]

I think you are correct in deducing there is a clock conflict. I have got the Dallas library and the RTC library working together by implementing the changes to the RTC library suggested by ForceTronics:

Reducing Power Consumption on Arduino Zero, MKR1000, or any SAMD21 Arduino Part 1

In the RTCZero-master/src/RTCZero.cpp file in your library directory make two changes:
comment out the line

//config32kOSC();

find the line:

GCLK->GENCTRL.reg = (GCLK_GENCTRL_GENEN | GCLK_GENCTRL_SRC_XOSC32K | GCLK_GENCTRL_ID(2) | GCLK_GENCTRL_DIVSEL );

and change to:

GCLK->GENCTRL.reg = (GCLK_GENCTRL_GENEN | GCLK_GENCTRL_SRC_OSCULP32K | GCLK_GENCTRL_ID(2) | GCLK_GENCTRL_DIVSEL );

These two changes swap the RTC library over to using the internal, less accurate but lower power timer.