Pandoc not finding Extra folder in Preamble

I'm trying to eventually use purrr to make multiple PDF documents. The Rmd renders fine when using default parameters and running directly from the template and using ctrl+shift+k in RStudio, but I'd like to produce multiple documents with different parameters. I'm using a R project and my working directory has a folder called programs and a folder called Enclosures. I would like the files PDFs to go to the folder Enclosures. The Rmd file in question has some extra TeX needed and are read in using the in_header and before_body commands. It seems that Pandoc isn't finding these TeX files. Here's a snippet of code:

                  output_dir = "Enclosures",
                  output_file = StateByStateDataset$FPEnclosure[i],

Here's the error:

"C:/Program Files/RStudio/bin/pandoc/pandoc" +RTS -K512m -RTS "\rtpnfil03/rtpnfil03_vol4/CSFACF/Statistics/Universe_For_Survey/Enclosures/Programs/Intermediates/" --to latex --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output pandoc15c812ec3620.tex --template "C:\Users\sazimmer\Documents\R\win-library\3.5\rmarkdown\rmd\latex\default-" --highlight-style tango --pdf-engine pdflatex --include-in-header "Extra\preamble.tex" --include-before-body "Extra\doc-prefix.tex" --variable graphics=yes --variable "geometry:margin=1in" --variable "compact-title:yes"
File Extra\doc-prefix.tex not found in resource path

Where should the "Extra" folder be for Pandoc to find it?

I'm not sure what was going on exactly but making a reproducible example made me realize maybe I had some relative paths wrong initially and it may have been as simple as that. Sharing an example of creating multiple parameterized reports here:

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