Hi Kenta,
I already try it, the PWM-duty can be changed in the interrupt function. Of course, this method is not work in PWM synchronization.
I don't know how you to update the FTM0_C0V. I use the following code. you can try it!
/* User includes (#include below this line is not maintained by Processor Expert) */
PE_ISR(FTM_OVER)
{
// NOTE: The routine should include actions to clear the appropriate
// interrupt flags.
//
FTM0_SC &= ~FTM_SC_TOF_MASK;
FTM0_C0SC &= ~FTM_CnSC_CHF_MASK ;
FTM0_C1SC &= ~FTM_CnSC_CHF_MASK ;
/* FTM0_C0V: ??=0,??=0,??=0,??=0,??=0,??=0,??=0,??=0,??=0,??=0,??=0,??=0,??=0,??=0,??=0,??=0,VAL=0x05DC */
FTM0_C0V = FTM_CnV_VAL(0x05DC);
/* FTM0_C1V: ??=0,??=0,??=0,??=0,??=0,??=0,??=0,??=0,??=0,??=0,??=0,??=0,??=0,??=0,??=0,??=0,VAL=0x05DC */
FTM0_C1V = FTM_CnV_VAL(0x07D0);
}
In this code, I just change the FTM0_C1V from 1500(0x05DC) to 2000(0x07D0), and the result is as follows, you will find the duty of C1 is changed.

If you still have question, please contact with me!
I wish my answer is useful to you!
Best regards!
Jingjing