I have found that when I have over 30 PEN files in the root folder, when I upload new files, instead of creating new files, older files are "updated." This causes both old and new notes to be merged on top of each other.
Have you checked the 'New Notepad' tick box when starting a new physical notepad? This is on page 1 of my Oxford stationery and unless it is done the new pages will overwrite those from the older notepad.
1) New notebook check box is essential. You must check it whenever you start a new notepad.
2) You can fix the notes that are overwritten, by using the History (clock icon) to scroll through the document, and separate the different pages. Edit the page, and Use the sliders on the bar at the bottom of the editing window to move "through time" to select the pages separately. This will select the pen strokes. I insert a blank page into the file, then copy and paste to the inserted page. You need to use the top and bottom sliders to get individual pages. Start with both top and bottom at the far left, then slide the bottom one to the little line that appears in the bar, this is a page marker. This selects just the first page. After pasting, move the top slider even with the bottom one (at the little line) and then move the bottom one again to the next line, or to the end of the bar. Repeat insert, copy and paste. I use the menus rather than the windows control-c, control-v key strokes. The keyboard seems to cause the software to error out after just a page or two.
3) I make it a habit to rename my documents after uploading from the pen with the date and title / subject. This prevents overwriting the documents on the next sync with my pen. In fact there is a setting in the options to choose the date and page number as the default document name. That also has helped prevent these little irritations.