Re: Publishing Reports and losing community reports.
Is you community content created in Test server? and you want to move them over to Live server? -- that is not possible out of the box.
As long as if you are replacing the app while publishing user created content will remain same. All user created contenct will be attached to the APP GUID. So if you delete the app or publish as a new app it wont have the community content.
Also at this moment there is no out of the box way to copy the user created content from one app to other.