I am so sorry that you have lost some of your progress in your work. The 'auto-save' in SketchBook is not 100% effective in saving files. You will need to always 'start' a new sketch to 'save it'.
One nice feature in SketchBook is to save your progress (versioning) of your file. You can review the steps noted here: http://help.autodesk.com/view/SKETPRO/ENU/?guid#saving
The basic workflow is:
a. Start a sketch.
b. Start a new sketch and save the sketch that you are working on.
c. Go back to the original sketch (in step a) via the Gallery.
d. Work on sketch (in step a) and then start a new sketch. At this point, you can 'Save a Copy" of your work.
David Lau