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1) Save the files you have changed in their changed state to a different folder, well away from your trunk directory.
2) (Make sure you have done step 1 first!) Revert the changes you have made to the files you copied in step 1)
3) Update the files you reverted in step 2)
4) Copy the files you copied in step 1) over the files you have just updated in step 3)
5) Make sure your commit comment describes what you have done and why!
HTH