When you first run Paperesso, you need to select a folder that will be used for storing and managing printouts and ink notes. Paperesso can only access printouts under this folder and its subfolders.
"Printout Folder" can be readily changed via Settings » printout folder.
Please note that Paperesso manages a printout with two separate files; one file for raw printout rendering data (currently only supports *.pdf) and another (*.paperesso) for page marking related data (ex. ink notes). Paperesso won’t make any change to the raw printout rendering data file; it’ll be used only for displaying the content of the original printout.
Please also note that Paperesso may create a temporary folder for managing new notes and changes. This temporary folder is automatically removed when you close the printout.
If you terminate Paperesso without closing the printout, the temporary folder may not be properly removed. However, when you re-launch Paperesso and open the printout again, Paperesso will automatically cleanup the folder and update the file (*.paperesso).