Are you driving the CE pin low after the write operation that writes the CH bit?

The data sheet describes how you must pulse the CE high to low to transfer data written in a sequence into the actual running registers inside the chip.

You may want to try this as a debug step...

When you go to stop the clock read out all the time registers and save them in the MCU someplace. Then write the CH bit = 1 to stop the clock.

When you go to restart the clock rewrite the full set of time registers from the saved copy in the MCU.

I would encourage you to look at using the burst mode for doing these reads and writes.

Michael Karas