R-markdown .docx output not reflecting changes in code, while PDF does.

RStudio IDE
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I have a project where I am printing a research manuscript in R-markdown and my co-authors want an output in Word-format.

Expected behaviour:
Output reflects the current version of the text.

Experienced behaviour:
While output to PDF reflects the current version of the text, output to word does not. Instead, I get an output that reflects an earlier version of the manuscript.

My investigations:
If I run the r-markdown code in a new project, it works as supposed to, but if I go back to the original project, it does not. If I save a copy of the file in the current project, it works as expected as well. I do not get any error messages besides some warnings:

1: In hook(x[i], reduce_plot_opts(options)) :
  Chunk options fig.align is not supported for docx output

My impression is that Rstudio do not read the current file at all, but knits something else. I find this odd since I have cleaned the cash, and since output to PDF works as it is supposed to. Any ideas of where the problem lies? Should I report this as a bug-report?

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