It's not only common but nearly universal when running in a new diesel engine to have to go back after a certain number of hours and re-torque the cylinder head - not only does the head gasket compress in the first run-in period but the cylinder head bolts themselves begin an ongoing process of elongation. This is especially true on diesels with their high compression. I have found on the smaller Yanmars that it is only necessary to run them for an hour or so after rebuild, before letting them cool off and going back in to re-torque the head. On the larger engines like Cummins, which is the only other make I'm really familiar with, it may take several hundred miles to achieve this "running-in" process - on the old B5.9 six cyl. workhorse, 500 miles is often thought necessary (depending on stage of tune - which can vary widely depending on application).

This re-torque is not specific to diesels but can be very beneficial on high performance gas engines as well. I used to work with Italian race cars and there were several of them with a reputation for blowing head gaskets (Alfa Romeo comes to mind) a problem that was later remedied by re-torquing the heads at a precise interval.