@Rypo –
That is correct. You cannot use the initial time from WRF for CMAQ. Most of the time, if we are using reinitialized run segments, we have some sort of overlap period (nominally 12 hours, but it does not need to be that length) that we “throw away”; in your case, the new segment would not pick up at 00 UTC, but it would instead by at 12 UTC (12 hours earlier).
–Tanya