Hi, Fatih,
I suppose that the second/minute/hour/month/year registers lose their value after you power off both the power supply from VDD pin and battery power supply from Vbat pin, you have to write the initial value to the second/minute/hour/month/year registers after you power on again.
This is LPC micro controller forum, for PCF2129 question, it appear you can post a ticket to the link:
https://community.nxp.com/community/other
Hope it can help you
BR
Xiangjun Rong