PDFs duplicated inside (and outside!) Paperpile folder

Started using Paperpile recently to evaluate it for my laboratory and was initially very impressed. However, I’ve just recently noticed that I have many duplicated PDF files with the filename paper_name (1).pdf, paper_name (2).pdf and so on inside the Paperfile folder.

Furthermore I noticed that some papers have been copied to the root directory of my Google drive, and it seems these papers also exist inside the Paperfile folder. Can I delete the PDFs that are outside of the Paperfile folder?

I just noticed these problems this morning after doing a Mendeley import last night.

I’m also not using any third-party apps such as GoodReader so there should not be any sync problems.

Any help on this would be greatly appreciated.

Please drop us a line through the support widget and we’ll follow up in detail.

Paperpile does not create files of the form papername(1).pdf. My guess would be you have imported a duplicate entry from Mendeley. If the meta-data is the same for multiple entries, the attached files will be named the same. When you sync your files to your file system using the Google Drive client for Mac or Windows, it will be disambiguated.

To find duplicates in your library, you can use the “Duplicates” filter on the right-hand filter list.

I’m not sure why some of your files ended up in the root folder. I can’t remember anyone reporting this problem in the past 2 years. As I can’t rule out that there is some complication introduced by the Desktop sync client, I’d suggest to check the Google Drive Webapp and see if these files are duplicated there as well.

1 Like

Thank you very much for your help.

I was expecting duplicates after the Mendeley import and merged them appropriately. My “Duplicates” filter was already at zero before discovering I had the disambiguated PDF duplicates in Google drive. Also the disambiguation varied from (1) to (8) for different files.

Today, I checked the Google Drive Webapp and was surprised that the duplicated PDFs no longer exist although what remains is the most recent disambiguated file (e.g. papername(8).pdf). I checked my Google Drive folder on my Mac and this is also the case. I’m not sure what caused this. I did do a Resync and Cleanup but I did not see any change after an hour or so, so I thought it did nothing. Maybe this is what got rid of the duplicates?

As for the duplicates appearing in my root folder, I just deleted those and it seemed to have no negative effect on my paper entries as they are still linked to the PDFs inside the Paperpile folder.

I’ll use the support widget now but I thought I’d chime in here in case someone also had a similar problem.

You don’t need a duplicate import to get (1) files in your Paperpile paper directory. I have noticed that if I upload a new version of a PDF that I have edited elsewhere to Google Drive, I get a duplicate file (leaves me with the old and the new version). This includes editing and annotating the file with external tools. Maybe it is actually a Google Drive bug, but it seems to occur only in the Paperpile folders.

How do you upload a new version? You need to replace the existing file in a way that the internal Google Drive ID does not change. Some third party programs don’t do that and that causes duplicates or missing files.

Most programs work correctly though including the official Google Drive desktop clients. If you edit a PDF in MacOS or Windows the changes will be synced correctly back to Google Drive and there are no duplicates generated.

I uploaded a new, modified, version of a PDF file using Google drive’s “upload a new version” button. And this is what happened: The article was a starred article, so it appeared once in its own alphabetic folder, and once under the starred folder (on the drive). I uploaded the new version under the alphabetic folder, but then a duplicate was created under the “starred” folder. To make sure I am not dreaming, I tried with another article, and the same happened. When I removed the star from the article, only a copy of the old version remained in the starred folder. Resyncing and cleaning up the directory did not get rid of the duplicate. These files are also shared in a shared folder on Paperpile, but I don’t think that is related (still I added the screen capture).

I’m having similar issues as the above post, though I did not manually add pdfs to Google Drive at any point:

My references were imported via syncing with Zotero online, as well as manually adding .ris files. I’ve resolved all duplicates, incomplete records, and “has attachment” references. In particular, I found that many “has attachment” references just had multiple of the same pdfs, presumably due to Zotero import, and deleted all but one version in those cases.

I’ve resolved all the above, and I am not using any other service online or on iOS that syncs to Google Drive (e.g., GoodReader, as advised against). But when I look into my Google Drive folder, I have up to 5 copies of the same pdf, named exactly the same. This is not the same as OP’s issue where duplicates were named with ___(1), ___(2), etc. These are named exactly the same. See attached screenshot.

I’ve provided one specific example, where the 3 copies of the pdf for O’Toole et al exist in GDrive, but on Paperpile it shows no indication of duplicate documents.

Lastly, Paperpile appears to duplicate folders as well? Though the pdfs that are inside the duplicate folders are different.


My Google Drive sync does this occasionally if I leave Paperpile open for more than 10 minutes or so. It did it again today. Is there any resolution to this? I know this post is 5 years old, but it still happens and that’s a little frustrating. I’m contemplating simply not having it sync so I don’t have to wade through the sea of papers and folders this shoves into my root directory.

I have this problem. I am not sure what causes it. Perhaps it is google drive rather than paperpile, or perhaps it is somehow something I did.

It is stubborn to fix it. I have a case where the second file (named …(1).pdf) is the correct version, but it is not the “main” pdf. After deleting the main pdf, I hoped that this second file could become the main one, but clicking “set as main” pdf only works for a moment. Refreshing the web page causes it to go back to what it was before. Further, the file got renamed to “supplementary.pdf”, and there is no way to rename it from the interface because it says “The file is named automatically according to your file naming settings”.

@paperbrain please select one of the papers this is happening to in your library, hit Ctrl+J and paste the resulting code in a chat message (bubble on the bottom right corner) or email (support@paperpile.com) so the team can take a look.