I've made the mistake (as indicated in the documentation) of continuing to develop in a branch that has already been merged into the trunk. What is the best way to preserve the work that I have done for another merge to the trunk?
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Check this prior question Reintegrate question and the referenced collabnet blog entry here.
The short answer: you're probably fine.
My recommendation would be to reintegrate/merge again and discard the branch. Alternatively, checkout a new copy and copy over your changes you want to preserve. You ought to be able to locate them in your working copy using 'svn st --recursive'.
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What I ended up doing was creating a new branch from the trunk from a revision after the re-integration. I then merged from the old branch to the new branch to grab the changes made post-re-integration. These merged into the trunk without the conflict complaints encountered when attempting to merge again to the trunk from the already re-integrated branch.

2NinerRomeo
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