I actually have a weird issue with Jenkins and 2 PHP projects. When deploying before launching the test suite, instead of having correct symlinks, Jenkins creates files containing the target path of the symlinks. I don't understand why it doesn't work only on 2 projects. It's OK on another very similar one. I tried to delete the working directories of those 2 projects, but I had the same result. Any hints would be appreciated.
Faced the same issue,
Jenkins JIRA saids that there is no option to override it, because they use external tool (Ant) for files. Also they claim that target system could not support symlinks at all.
You can only exclude symlinks from deployment and then create them manually.