If your files are saved in the local, just do as below:

1. Enter the reading page, make comments to change your PDF files. All your changes will automatically save in the file. 
2. Or you can tap More icon and choose the Save button to preserve changes.

3. Or tap  button, then all your changes will be saved.

If your files are from the third app like email, you should download it first and then you can search it in Local.