I have seen many people who tend to ignore the “Skipped” messages that are sometimes displayed when you do a merge with subversion:
The “Skipped” message means that the merge operations wants to create or modify a file but that file already exists in your working copy and is not under version control (added to the repository:This can easily happen if you do a forward merge from trunk to a brunch and revert your local changes to the working copy (maybe because some manual merges went wrong). The revert command will leave new files as orphaned files in the working copy.
Don’t ignore those warnings! If you commit a working copy with “Skipped” warnings and do a backward (reintegrate) merge from branch to trunk, subversion will delete the formerly skipped files from the trunk! As a rule, you should never ignore “Skipped” warnings and if they occur fix the root problem then repeat the merge on a clean working copy.