Just to be sure I understood right: you had the project completed in an air cut, buit when cutting into material the cut randomly stops?
My thoughts would be: If your cut completes in an air cut it shouldn’t be your gcode. If it stops under load randomly, it sound to me like interference. Have a look here, where I summarized my experience with that.
Another question: How many hours to you have on your router? Are your brushes ok?