Issue solved, see answers for details.
I would like to run some code (with knitr) on a more powerful server and then maybe have the pos
I wonder if in addition to @Yihui's answer if the process of copying from one machine to another changes the datetimes on the files so that they look out of date even when nothing has changed.
Look at the dates on the files involved after copying. If you can figure out which files need to be newer than others then touching them may prevent the rebuilding.
Another option would be to just paste in the chached pieces directly so that they are not rerun (though that means you have to rerun and repaste manually if you change anything in those parts).