Yes. In EndNote, highlight the citation for any reference that has a PDF attached to it and look at your preview pane, located either on the right-hand column of the EndNote screen, or in a pane across the bottom. If the PDF is not already showing, select the PDF tab, and then click the "Open PDF" icon to view at a larger size and to add highlighting or comments. When you click the small "x" to close the PDF, you should be asked whether you want to save those changes, and they will then be there the next time you preview or open that PDF.
Please note, however, that the changes may not be saved if you open the PDF using EndNote's "Open File" icon in the row of menu icons across the top of the screen, which opens the file in Adobe Acrobat rather than within EndNote's own PDF function.
In other words, using this icon (circled in red below) will allow you to save the changes you make to a PDF within EndNote:
However, using this icon (circled in red below) may not allow you to save the changes you make to a PDF, as it may open the PDF in Adobe Acrobat instead of within EndNote:
