Thank you for your advices !
I know what I'll do next time. for this PCB, I already have an RTC, but didn't anticipate this need, I only have I2C and power connected.
So, what I did is to predict how many ms have passed during sleeping mode and correct the millis() counter at wakeup, based on WDT clock. As the precision is about 10%, I check the new millis() counter with my RTC, and correct it if there is more than 2s of desync.
I added a dynamic coefficient to correct the millis() counter from WDT, I increase or decrease this coefficient each time I need to sync millis() with RTC, depending of how often I have to resync, so, after some resync the correction from WDT is quite accurate (enough for my needs).
Another question about TIMER accuracy and consumption :
As I don't use any PWM, I tried to power off TIMER1 and TIMER2 permanently since only TIMER0 is needed to micro and millis counter. But when I do that, it's like TIMER0 is not accurate, it's like it uses the same clock as WDT.
Do you know if TIMER0 depends of a clock used by TIMER1 or TIMER2 ? If yes, which one, and which one I can stop permanently to reduce consumption and keep accurate TIMER0 ?
Thank you.