The circuit seems to be ok. According to the datasheet those are Zener diodes so the design is correct. That leaves the issue to be most likely power related. Have you seen section 4.13 of the Edison module Hardware guide Compute Module Hardware Guide for Boards and Kits? There you’ll see:
The PMIC can be programmed with a charge voltage of 2.5, 3.0, 3.15, or 3.3 V. The charge current is programmable to 10, 50, 100, or 500 μA.
It is also stated in the document that the minimum RTC retention voltage is 2.05V. If the voltage drops below this level the RTC is likely to display wrong values, loose the configuration or return to the default settings once it reconnects. Make sure the RTC is properly powered at all times. How much power are you supplying through RTC_PWR?