# File links not updated after "Copy linked files to folder" and cleanup — PDFs still point to original paths

**URL:** <https://discourse.jabref.org/t/file-links-not-updated-after-copy-linked-files-to-folder-and-cleanup-pdfs-still-point-to-original-paths/9088>\
**Category:** Help\
**Created:** [May 3, 2026, 2:55am UTC](https://discourse.jabref.org/t/file-links-not-updated-after-copy-linked-files-to-folder-and-cleanup-pdfs-still-point-to-original-paths/9088 "2026-05-03T02:55:06Z")\
**Posts on this page:** 2\
**Page:** 1

<div class="post-metadata">

**Author:** ![hasibagen](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.jabref.org/hasibagen/32/2565_2.png) [@hasibagen](https://discourse.jabref.org/u/hasibagen)\
**Post date:** [May 3, 2026, 2:55am UTC](https://discourse.jabref.org/t/file-links-not-updated-after-copy-linked-files-to-folder-and-cleanup-pdfs-still-point-to-original-paths/9088/1 "2026-05-03T02:55:06Z")

</div>

## Summary

I imported PDFs from multiple scattered directories into a single `.bib` library  
via JabKit (`convert --input-format=pdfMerged`). The `file` fields contain  
absolute paths to the original locations (deep nested Zotero-style directories).

I want to consolidate all PDFs into one folder next to the `.bib` file. I tried  
the built-in tools, but the file links in the database are not updated — opening  
a PDF from JabRef still tries to access the original path.

## Steps to reproduce

1. Import PDFs from multiple folders into a `.bib` library using JabKit:  
jabkit convert --input= --input-format=pdfMerged  
–output=library.bib --output-format=bibtex  
The resulting entries have `file` fields like:  
file = {:/home/user/data/paper/ref/rsa\_method/2019\_Popal …/origin.pdf:PDF}

2. Open `library.bib` in JabRef.

3. Set the **Main file directory** in Library Properties → General.

4. Click **Library → Copy linked files to folder**. Files are copied to the  
target folder.

5. Run **Quality → Cleanup entries** , enable file-related options:

- “Move to file directory”
- “Make paths relative”
- “Rename files to match citation key”

1. Save the library.

## Expected behavior

After step 5, the `file` field in each entry should be updated to point to the  
new location. Opening a PDF from JabRef should use the new path.

## Actual behavior

The files are physically copied to the target folder, but the `file` field in

## What I’ve tried

- [Copy linked files to  
folder](https://discourse.jabref.org/t/the-function-of-copy-linked-files-to-folder/1957/14)  
— copies files but doesn’t update links
- [How to save PDFs to different  
folder](https://discourse.jabref.org/t/how-to-save-pdfs-to-different-folder/2984/6)  
— setting main file directory doesn’t trigger link update
- [GitHub #121](https://github.com/JabRef/jabref/issues/121)  
— related but doesn’t address the link update issue
- [Prevent JabRef from auto-renaming and moving files]([https://discourse.jabref.org/t/prevent-jab](https://discourse.jabref.org/t/prevent-jab)  
ref-from-auto-renaming-and-moving-files/2596/11?u=koppor)
- [Move folder with PDFs and have JabRef reconnect]([https://discourse.jabref.org/t/move-folder-wi](https://discourse.jabref.org/t/move-folder-wi)  
th-pdfs-and-have-jabref-reconnect-links-to-them-automatically/2285/13)  
— closest match, but the solution didn’t work for my case
- [How to change automatically links of pdf files - #2 by Siedlerchr](https://discourse.jabref.org/t/how-to-change-automatically-links-of-pdf-files/9041/2)

## Environment

- JabRef 5.15–2024-07-10–1eb3493
- Linux 6.17.0-22-generic amd64
- Java 21.0.2
- JavaFX 22.0.1+7

## Question

Is there a correct workflow to both copy PDFs to a single folder **and** update  
the file links in the database? Or is this a bug where “Copy linked files to  
folder” doesn’t trigger the link update?

---

<div class="post-metadata">

**Author:** ![Siedlerchr](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.jabref.org/siedlerchr/32/216_2.png) [@Siedlerchr](https://discourse.jabref.org/u/Siedlerchr)\
**Post date:** [May 3, 2026, 5:36pm UTC](https://discourse.jabref.org/t/file-links-not-updated-after-copy-linked-files-to-folder-and-cleanup-pdfs-still-point-to-original-paths/9088/2 "2026-05-03T17:36:54Z")

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Thanks for your issue. We will look into this! Have you tried the latest development version from [builds.jabref.org](http://builds.jabref.org) ?