Update: This issue was resolved through Jetpack email support.
For those who may have similar issues and find this thread in the future, the following is FYI:
Turns out this was this issue:
https://jetpack.com/support/wordpress-com-stats/missing-stats/
We got support by filling in the form here:
https://jetpack.me/contact-support/
So disappointing that 5 days have gone by with no response…
