As a default Citavi does not save annotations in the PDF file. Instead, annotations are saved in a transparent layer above the text. The PDF is not changed in any way. This has two advantages. First, editing and saving annotations is faster, especially if the PDF is saved on a network drive or in the cloud. Second, PDFs can then be used by multiple people each saving their own individual annotations.
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 an external program will be saved in the PDF file. However, only highlights will be displayed in Citavi and will be available for further editing. If you open a PDF in Citavi that was annotated in another PDF reader all the notes, arrows, lines, etc. will be ignored and only the highlights will be copied into the Citavi layer. They'll appear in the same color as in the external reader but will be displayed as underlines instead of highlighted text.