If nothing inside the home was altered you should not be getting a smell. Personally I'm confused as to why the repair person would have left the original line there and ran another one through a new hole. I would have pulled the old line up, ran the new line (in PVC) and used the same hole in the septic tank instead of creating a new one. Did he seal up the hole in the tank from the old line?
When a person has a blockage in their sewage system they often try to fix it themselves by adding an acid or a base such as Drano in an attempt to dissolve or dislodge the problem. These chemicals can get into the plumbers eyes when the sewage is splashed during the repair. The plumbers skin during the repair does come into contact with the sewage water. The owner of the toilet might not report to the plumber they have already tried Drano a highly caustic base .