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https://issues.apache.org/jira/browse/PDFBOX-4640?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16919794#comment-16919794
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Tilman Hausherr commented on PDFBOX-4640:
-----------------------------------------

You didn't mention that you're flattening, i.e. that this isn't a document you 
loaded and then merged. Please try saving the modified document and then reload 
it. If it still happens, please try with the command line utility and attach 
the "second" document.

> PDF Annotations missed when merging documents
> ---------------------------------------------
>
>                 Key: PDFBOX-4640
>                 URL: https://issues.apache.org/jira/browse/PDFBOX-4640
>             Project: PDFBox
>          Issue Type: Bug
>          Components: Utilities
>    Affects Versions: 2.0.16
>            Reporter: Daniel Martin Garcia
>            Priority: Major
>              Labels: merge
>         Attachments: highlighted pdf.pdf
>
>
> Hi,
> There is a bug when PDFBox merges documents with annotations, but the 
> annotation opacity is not 100%. If the opacity is less than 100%, the 
> annotation is lost.
>  
> I attach a document with an annotation which opacity is 60%, if you create a 
> test to merge this pdf with other PDF, the annotation won't be in the merged 
> pdf.



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