They might still contain data that groups those multiple accounts together though. Eg everyone in X university gets the same watermark.
So if you have a watermark that associate files with the time they have been downloaded, and download it from multiple networks etc. at the same time, and remove the diff from these versions, you'll still have the time-based watermark in the resulting file, so you'll leak when you downloaded it.
Your tool can be as crude as running the document through pdftotext and only keeping the text output. It can just throw away all these possible side channels that are not relevant to the actual content.
Others mentioned other more sophisticated side channels, as rewording sentences, but I'm sure authors would not welcome that.
1. Download the content with N accounts, preferably from different networks.
2. Run your watermark removal tool on each downloaded data independently.
3. Check if the processed outputs are bit-for-bit identical.
Have fun writing watermark removal tools.