The way the files should be processed is clear in the operation manual. In the page 3 of the operation manual for applicants on or after May 4,2013 (http://www.cic.gc.ca/ENGLISH/RESOURCES/manuals/op/op06c-eng.pdf) is mentioned:
What this chapter is about
This chapter describes the processing of applications for permanent residence submitted by applicants in the Federal Skilled Worker
Class, and received by the Centralized Intake Office(CIO) in Sydney, Nova Scotia on or after May 4, 2013.
Note: Information on processing applications for permanent residence under the Federal Skilled Worker Class received before May 4, 2013 is provided in
OP6, OP 6-A and OP 6-B.
The applications which have been submitted before May 4, 2013 should be assessed according to the operation manual 6B (http://www.cic.gc.ca/ENGLISH/RESOURCES/manuals/op/op06b-eng.pdf)