I solved this problem by using an Invoke Code activity. Before the core logic begins, I check if the PDFTronC.dll file is in the working directory. If it is not, I copy the file over from the Y Drive to the working directory. Upon completion or failure of the process I then delete this file to be safe.
A janky solution to meet the jankiness of UiPath.
string sourcePath = @"Y:\myFolderDirectory\PDFNetC.dll";
string destinationPath = Path.Combine(Environment.CurrentDirectory, "PDFNetC.dll");
if (!File.Exists(destinationPath))
{
File.Copy(sourcePath, destinationPath);
}