I\'ve been doing some reading about continuous integration recently and there is a scenario which could occur which I don\'t understand how to deal with appropriately.
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In my experience with CI, the way that you should keep your feature branches up to date with the main line changes as others have suggested. This has been working me for several releases. If you are using subversion make sure you to merge with the merge history enable. This way when you are trying to merge your changes back to line it will only like you are merging the feature changes to line, not trying resolve conflicts which your feature might have with the main line. If you are using more advance VCS like git the first merge will be a rebase where the second will be a merge.
There are tools that can support you to get thins done more smoothly like this Feature branches with Bamboo