Is your editor locking files? Brackets does not lock files, don't know about other editors.
Edit: Do you have Koala configured on the theme folder or the entire project directory? You should not let Koala touch anything in the deployment folder because that could cause conflicts too. In Koala, click on the file and you can turn off autocompile for anything in the deployment folder.
Note that you can rename items in the Koala project list, or they would all be named 'theme'...
Is your Node Modules folder added to the SVN ignore list?