I've just check my original tracking code still "live" and from the Piwik 1.11 release and the one suggested in Admin=>Manage Websites.
It's almost the same but saw one bigger difference :
var u="//stats.mysite.com/"; (Piwik 1.11)
var u=(("https:" == document.location.protocol) ? "https" : "http") + "://stats.mysite.com/"; (Piwik 2.15)
I never experienced loss of data from this difference but I was wondering if Piwik should alert us if JS tracking code should be revised in our inclusions?