We had a similar issue in Sparks, where a child completed the HangGlider as a kindergartner and parents chose to keep him in kindergarten again this year.
We chose to delete the entrance booklet and HangGlider book that were completed last year, and then reassign the entrance booklet and the HangGlider book for this year.
With Cubbies, you could do something similar:
1. Delete Apple Acres yr 1 completed in their first year
2. Delete Apple Acres yr 2 completed in their second year (after writing down date last section was completed for last year) - Note: This will become yr 1
3. Add Apple Acres yr 1 and mark it "done" in history mode, using the date from #2.
4. Add Apple Acres yr 2 and use for the current year.
5. Delete the handbook completed in the first year and then reassign it for this year.
This is how I would choose to do it in order to have the entrance booklets sequences correctly for yr 1 & 2. I would treat the first year this child did Cubbies as non-existent to put them on track.
Hope this helps.