epstopdf - EPS files with same name

My project has EPS files of the same name saved in a nested folder structure. For example, I have files ~/folder/sub1/foo.eps and ~/folder/sub2/foo.eps. In my tex file, I have the following epstopdf setup:

usepackage{epstopdf}
epstopdfsetup{
suffix=,
outdir=./include/eps_to_pdf/
}

I then include the two figures as follows:

begin{figure}
includegraphics{../../folder/sub1/foo}
end{figure}

begin{figure}
includegraphics{../../folder/sub2/foo}
end{figure}

However, the figures both compile as the first figure. As I understand, this is because the first EPS with this name is converted to PDF and, because there now exists a PDF with that name, epstopdf will skip over the conversion process for any future EPS with that name.

Thus, my question is: what are the recommended workarounds for this? Ideally, there would be an approach that doesn’t require converting the EPS to PDF every time I compile. However, this is preferred to renaming my files because this is not an isolated example.