Looking at the chunk options here, https://yihui.name/knitr/options/#plots, more specifically fig.process:
fig.process : ( NULL ) a function to post-process a figure file; it should take a filename, and return a character string as the new source of the figure to be inserted in the output
You could probably write a function that removes the numbering and then copies/moves the new file to the figure folder
If all the figures only have -1, then something like this should work (tested on PDF template).
knitr::opts_chunk$set(
fig.process = function(filename) {
new_filename <- stringr::str_remove(string = filename,
pattern = "-1")
fs::file_move(path = filename, new_path = new_filename)
ifelse(fs::file_exists(new_filename), new_filename, filename)
}
)