Hello @kyf,
I saw the BCTU options for configuration but I didn't find any option for link with "flag generation" on PWM channel.
It seems to me that BCTU just work with ADC, doesn't it?
For example:

For it, I understand that we must work in "Internal Trigger" section, because the another sections are "Bctu ADC notification" (the name itself says it all, ADC notification), "Bctu LIST items" (if BCTU configured with conversion using list of channels in ADC, we must configure this section) and "Result FIFOs" (If configured the ADC conversion result as FIFO, we must configure this section).
So what was left was the "Internal Triggers", and all options are tied with ADC, like, if is the single conversion or not, the data destination of conversion, and so on...
Did you see my configuration using Emios_OCU? The notification worked in underflow/overflow, but not in the same channel configured on PWM. Maybe this is the way but I think that there is some simple detail disturbing it.