CRA indicates that s. 163(1) penalties for 2014 and prior will not be reduced to reflect the more favourable post-2014 penalty calculation

The amended version of s. 163(1) imposes penalties for the 2015 and subsequent taxation years in accordance with a more favourable formula than previously. CRA will not exercise its discretion under s. 220(3.1) to reduce penalties assessed for the 2014 and prior taxation years to this more favourable basis, and instead will only apply its usual (somewhat onerous) criteria for penalty relief.

Neal Armstrong. Summary of May 2016 Alberta CPA Roundtable, Q.4 under s. 220(3.1).