Hi Megan,
Thanks for your reply.
The new files correspond to a new WRF simulation; not a restart. We reinitialized WRF every 5.5 days where the first 12 hours correspond to spin-up time and are discarded.
We just found this post where a similar issue was reported:
It seems that what we need to do is run mcip in 5.5-day increments that include the 12-hr WRF spin up files that we were originally discarding.
We will give this a try.
Thanks.