A few things to point out here:
1.) As soon as you do any Apply Config from the Core Config Manager, those changes could go away. As of 2014R1.2 an Apply Config will overwrite any changed config files (as opposed to the old method where it overwrote them regardless). So even if you just change one config option the others that you made to the .cfg files will be blown away.
2.) I would be careful with making global changes that way, as some other plugins might have a "-v 2" switch for other reasons, or a different service might run the same plugin and still need that switch and it has now been changed to just "2". And as above, any changes in the CCM will overwrite this.
Like I said before, this is a change that needs to be done carefully and with some forethought. It can be done, but it might not be one easy step. Let me get back to you in a bit and we can discuss it more.
Update: A better solution if you are comfortable working on the CLI (which it seems you are) is to do a very precise replace like you did (making sure to only change what needs to be) and copy out those new configs to a /tmp directory. Then delete the existing services in the CCM and follow this guide to re-import the changed configs:
http://assets.nagios.com/downloads/nagi ... ios-XI.pdf