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patchSynctex doesn't patch the .Rnw files ; it patches the corresponding .synctex[.gz] files...
Indeed, this will have trouble with included parts (the "right way" to do this is to use children chunks, see the docs).
But Yihui Xie has decided not to support concordance with these children chunks. See his comments in the issues of his github repository. There is little one can do without forking knitr. And I won't do it (this would require much more of my time...).
Given the current complexity of knitr, its wide non-\LaTeX targe audience (mardown seems dominant these days) and the narrowness of this potential feature, I can understand Yihui Xie's decision...
So, unless you have new ideas about this old thorn in my flank, I close this issue.
patchSynctex() does not patch Rnw files included with \input{} or \include{} in the main Rnw file.
Working example: knitr-with-input.tar.gz
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