For example, should I only update the changing digits, or update the entire zone that contains the time?
Update the entire zone. This is faster, as only one "fast partial update" is needed. You can even update the whole display with "fast partial update", using setPartialWindow(…) with screen dimension.
When experimenting with partial update, I have seen that the new digits are not as black as they were on the first time I displayed them. Is it normal or is there a better way to do this?
The demo code for the GDEW029T5 uses the same wavetable as the GDEW0213I5F. But this wavetable may not be optimal for avoiding fading. I have not yet experimented with VCOM values, and experimenting with wavetable modification is outside of the scope of my current work for this. I see fading when powerOff() has not been called after partial update. Calling powerOff() may help, for updates every minute.
You can decide if you rather like a version soon, and maybe later optimization, or wait until I have done more extensive tests.
Did you tell us which is your other e-paper display?