Oh interesting, I could’ve used this tool before. The best I found before was pdftohtml as well. Generally converting from PDF is awful. PDFs internally are more or less postscript which is like a little programming language that describes how to print things, as opposed to a markup language, so reverse-engineering the content can be whacky. If you haven’t used pandoc before that’s very useful in general (though not for PDf-to-other formats, you’ll need specialty tools like this) More on reddit.com

The problem you're running into is the simple fact that PDFs store their information in a very different fashion than HTML documents. HTML documents pay more attention to content than layout. This includes organizing text into paragraphs and lines, and results in those documents rendering all sorts of layouts automatically. Most modern editable documents are based on XML, which is closely related. These documents convert pretty neatly to just about anything else, because the files are pretty much just instructions on how to display them. PDFs don't think about any of that. They rank layout above absolutely everything else, and that usually means things like breaking paragraphs up into individual lines, putting images on exactly the right spot every time, and generally making sure everything looks the same, regardless of what software or device you're using to open the document. Even if the PDF was generated from an XML-based document, the organizational information that lets a webpage render on-demand is discarded in favor of the layout data. Sometimes layout information might be included underneath everything else (like when a scanned PDF is made searchable - what's happening is that an OCR tool is reading the text and creating invisible lines of textual information underneath everything else), but there's no guarantee your converter of choice can properly interpret this information even when it is present. Now, there are some very spotty ways of working around this. Both Microsoft Office and Google Drive will attempt to read a PDF and make some assumptions about layout so that they can create a workable document from it, and some OCR solutions are getting better at doing the same. When these work, those generated documents translate easily to HTML, but that intermediary step is always going to be necessary for a PDF. More on reddit.com

The best way is probably to use PDF.js More on reddit.com

PDF is one of those things programmers avoid like the plague, up there with timezones and eager grandparents. PDF is, in and of itself, a programming language. Under the hood, it has lines of code to write each component to the document. There are many, many ways it can write things to the document, so two documents could render the same but have vastly different file sizes. In addition, each PDF creator (be it adobe, libre office, Microsoft office, chrome, etc.) May save the same mark up differently from the others. This leaves a lot of room for error in programmatically reading, editing, and writing a PDF document. There exist projects to handle it, like pdf2htmlEX which I'm told is good, but is no longer being maintained. You can also look at Libre Office's Draw program, which allows for reading, editing, and saving PDF files. It is, as a GNU program, open source. You could, maybe find some ideas of how to do it from this. With 2000 PDFs, however, the only feasible way to do it is programmatically. You would be best served studying how PDFs work and building your own library to handle them, maybe using the above projects as a baseline, otherwise Draw may support saving a PDF as a HTML document, in which case you'd just have to do that 2000 times. Either way, I wish you luck. This isn't an easy task. More on reddit.com