By default, Citavi does not save annotations directly to the PDF file, but rather to a separate layer that overlays the PDF, leaving the original file unaltered.
The PDF itself will only be changed if you export your annotations to the PDF. After that, you can view your highlights in an external PDF reader. This is useful if you want to give the PDF file to another person or if you want to continue working with it in an external reader on a tablet or other device.
All annotations made in external PDF readers are saved, but only the colored highlights can be viewed and edited in Citavi. If you open a PDF in Citavi that you have annotated with another PDF reader, all notes, arrows, lines, etc. will be ignored. Only the highlights will be copied into Citavi's layer.