A good diagram with the step/base flashing and cap/conterflashing (local term here)…but does the AHJ allow combustibles like “ice and water” barrier to be installed directly on the chimney?? Usually framing/sheathing members require 1/2-2" clearance.
Scott, if you say these shingles were originally in contact with the flashing, then movement is the only feasible explanation. 3/4 of an inch would be hard to see in the attic without a laser beam or string line. Log rafters may have been replaced with the last roof, in which case simple shrinkage could cause a drop in the roofline. Poor notching, gaps at the ridge, rot from leaky flashing?. You have probably called for further evaluation, which is about all you can do in a normal home inspection anyway.
The roof is all log and hand hewn beams with mortise and tenon joints pegged togather. There was one beam about 14’ away that had a check possibly even a split all the way down the middle of the 8" beam. I think this one was too far away to affect the area in question, but I do think the roof has dropped in the last 17 years.
Brian, I think the flashing was a pretty good job, they reflashed when they rebuilt the chimney and daylight was not visible from the attic space (seen that plenty of times).
Anyway, I did call for further evaluation, I just wasn’t comfortable with it.