If you are using a source control application, then you must check out the messaging files before you generate new ones.
In my case I have the messaging project file pointing to my project's folder where I want those files and never had a problem with the generation process as long as I have them checked out before. I do a nightly backup and always check in all files before the backup to be on the safe side.
I usually generate the XML files into a commom folder in the network, and then I copy the files into my local project "Localization Messages", which will trigger the source control to ask me to check them out.
Thanks!
http://visualstudiohacks.com/tips/options/add-an-existing-file-to-a-project-without-copying-it/ Keith Chisarik