Kumar,
I spoke falsely earlier: upon further investigation, the issue type is coupled tightly with the plugin, not editable on a quality profile (although in my opinion it would still be nice for a changelog item somewhere when that changes, as evidenced here it does cause some confusion). This is different behavior than when issue severity changes on a rule (existing issues get updated with the new severity). I'm sure there's a reason it's like this today: the measure changes would be noisy if all issues associated to a rule changed, but it does seem inconsistent.
(I'd also add that if you can change the issue type on an individual issue, it would make sense that you could edit that in a quality profile as well, but that's not the case today.)
What you can do instead of deleting projects when you run across this is utilize the "Bulk Issue Change" tool. After drilling down to the rule in the [Individual Project] > Issues section of your your remote instance, click on the Bulk Change button and then use that to change the issue type on all those individual issues. Next time you scan, all your measures will be updated (unless you update to SonarQube 7.0, where measures like that are live!)
Can I ask why your scanning on a local instance first? I'm curious what your reason for that is (I imagine it's getting around the lack of preview mode in 6.7+?)
Colin