How to Merge Annotated PDFs Without Losing Markups

Merging PDFs with annotations often leads to lost or flattened annotations. This guide explains why that happens, how to merge annotated PDFs with Xodo PDF Studio, and how to avoid common mistakes that cause annotations to disappear.

Merging PDFs is usually a straightforward task until annotations are involved. This is because many tools treat annotations as visual elements instead of structured data. When merging PDF content, those markups may disappear, become uneditable, or be permanently flattened into the page.

This is a common problem for legal teams reviewing contracts, AEC professionals confirming floor plans, and editors involved in multiple feedback rounds.

A merged PDF that looks fine but no longer contains usable comments can bring review workflows to a halt.

In this guide we'll teach you how to merge two annotated PDF files without losing any markups. You'll learn:

• What happens to annotations when you combine PDFs
• How to merge two annotated PDFs using Xodo PDF Studio
• Common mistakes to avoid when merging PDFs with markups
• Answers to common questions on merging annotated PDFs

What happens to annotations when you combine PDFs?

When you merge multiple PDF files together, markups and annotations can be treated in one of three ways. When you merge PDFs with annotations, it can either generate a PDF with editable annotations, a PDF with flattened annotations, or the annotations may be deleted from the PDF entirely.

Here's what can happen in a bit more detail:

• Editable annotations preserve comment data and authorship. You can still open comment panels, reply to notes, filter by reviewer, and continue collaborating.
• Flattened annotations will turn markups into static content inside the PDF. The annotations can't be replied to or edited.
• Some tools may drop comment layers during the merge process altogether, deleting any comments or markups completely. This is usually the case with basic PDF tools.

Advanced PDF editors, like Xodo PDF Studio, can preserve the PDF annotation objects and metadata across the merged files.

How to merge two PDFs with annotations using Xodo PDF Studio

To merge two PDF documents with annotations, you will need to:

1. Download and install Xodo PDF Studio.
2. Go to the Convert tab > From Multiple Files.
3. Click on Add Files or Add Folder to upload the annotated PDFs to merge.
4. Customize your settings and arrange your selected files in your desired order.
5. Click on Start...
6. Save the merged PDF to your computer.

All your existing comments, highlights, sticky notes, annotation formatting and markups from the other files will remain editable in the final merged document.

Reviewer names, timestamps, and threads are preserved, making it easy for you to review, reference, and continue collaborating inside the same PDF document.

Why Xodo PDF Studio works for merging annotated PDF files

Xodo PDF Studio treats annotations as objects and handles document structures as needed. Its focus on getting the structure right means you can count on it to reliably merge annotated PDFs.

This matters for professionals who need:

• Comment lists and panels that stay intact after the merge
• Highlight layers that remain selectable
• Markups that can be filtered or replied to
• Files that remain standards‑compliant

With Xodo PDF Studio, comment threads are merged into one file without losing context.

Common mistakes to avoid when merging PDFs with markups

Even if you're using the right tool, just a few common mistakes can cause all your comments and markups to vanish when combining multiple PDF files.

• Flattening too early
  Flattening annotations before merging removes your ability to respond to or manage comments. Only flatten your PDF files once the review process is done.
• Printing to PDF
  When exporting your annotated PDF, don't use the "Print to PDF" functionality as this will flatten PDFs.
• Losing layer information
  Some tools get rid of annotation layers when they combine multiple PDF documents, which can result in losing your highlights or comments. Be sure to keep an original file as a back up.
• File version confusion
  If you're merging outdated annotated files, you can reintroduce resolved comments. Make sure you're working with the current PDF version of your file.
• Using outdated PDF tools
  Don't use old versions of PDF tools. Outdated versions of PDF tools may not work to merge all the comments in your PDF files properly.
• Using free or basic online tools
  Depending on the tool, this method will likely merge the visuals only, stripping comment metadata and reviewer details. Use an advanced tool or a PDF editor to retain editable annotations.

Frequently asked questions

1. Can I merge two PDFs with comments without flattening them?

Yes, if you have a PDF editor like Xodo PDF Studio its possible to keep the comments intact and even merge them into a single document without having to flatten them.

2. Will highlights remain editable after merging PDFs?

Yes, they will. Xodo PDF Studio is a powerful tool that will let you edit and select your highlights even after you've merged all the PDFs into a single PDF.

3. Do merged PDFs keep reviewer names and timestamps?

Yes. If you merge PDFs with advanced PDF editing software, like Xodo PDF Studio, you'll keep all the annotation metadata, including author and time data from multiple documents.

4. Why do some tools remove comments when merging PDFs?

Many basic tools flatten or discard annotation layers to simplify the output process. They don't have the functionality to handle the complexity of comment layers.

5. Is flattening annotations ever recommended?

No, it isn't recommended to flatten annotations if you want them to remain editable. Flattening is useful only for when you have the final version of the PDF and don't need to make additiinal changes.

6. Can I annotate PDFs after merging them?

Yes, you can. Once your annotated PDFs are merged into one PDF file, you can still annotate the document, add new comments, and collaborate with multiple people.

7. Does merging PDFs increase file size?

Yes, it probably will. The file size may increase slightly because of the content and annotation data of individual pages being combined into one document.

8. Can you merge annotated PDFs with macOS Preview app?

Yes, you can. Open an annotated PDF in the Preview app and drag in the second annotated PDF into the thumbnails sidebar. Then save it to preserve the markups and imported comments.

Merge PDFs confidently without flattening markups

Merging PDFs that already contain annotations requires more than a basic combine function.

If your work depends on accurate feedback and clean document versions, using Xodo PDF Studio can retain your annotation data and merge comments in one document.

For reviewers, legal teams, and AEC professionals, this means avoiding redoing the work, protecting the feedback you've collected, and maintaining clean, review‑ready documents.

Try Xodo PDF Studio and keep your annotations going with ease.