What is the problem?
If the run is paused for some reason and during that pause the print head is raised or lowered by command then a resume is done, the head returns to the point in the run where the pause occurred in the X and Y only. It does not know the Z has been changed.
This is something my previous printer prog. did not fail to account for.
What did you already try to solve it?
Ask if someone could look into a little bit of code so that the resume button can be pressed and be confident the print head will resume the job in all three axis' where it left off.
Additional information about your setup (OctoPrint version, OctoPi version, printer, firmware, octoprint.log, serial.log or output on terminal tab, ...)
I don't think the setup has any influence on this problem other than Octoprint version is 1.3.10, OctoPi hasn't been logged into since setup as I've lost my login info.