When using the PCF8563 for the second time, there will be a time-jumping situation. Why? (Set 1 second, after 1 second delay, read out is 3 seconds)
Please show the schematic and complete operation step about your issue.
You can write then read 10s to 02H register to make sure the actual data again!
According to your suggestion, I have operated. Write 10s to the 02H register, then read the value of the 02H register, and read 11s.
10s is just an example. The wrong ones may be other seconds.
I have sent the schematic and the step to you. Is there an answer now?
Can you give the detail parameters of components in you schematic?
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