Can you take a .pdf file and convert it to Advanced PDF format? If we were to get nice Estimate, Invoice docs designed, they'd be given to us as PDFs so need easy way to convert to advanced PDF and then add the logic and fields needed

Short answer I'd say no. The PDF is a binary file format so you would struggle to pick apart the formatting and translate that to a pdf template. You're effectively trying to reverse engineer the PDF, unless there's a tool you can find online that'd break it down to freemarker with a splash of BFO syntax I'd say you're going nowhere with that. The best you can hope for is to try and replicate the layout based on how it looks, potentially a long slow process.