Yes, you should be able to check in later, with cutoff times adjusted to reflect the new flight time.
I recently had a delayed flight from SFO-HKG and I got a notifly message like yours and I checked in around 70 minutes before the "new" check in time which was only around 25 minutes before the "original" check in time and I didn't have any issues (though I was one of the last to check in)