Unfortunately an OpenSource nightmare scenario has hit FTPSync with 1.3.07: It uploads files even in download mode.
This is I have fixed in the git head at savannah, and I just published a hotfix release bug #38906 with git commit 65c0a4fed73b719352e5fa00096a4081d9cc3a63, but I actually recommend to use the re-released ftpsync-1.3.06-1 based on the last clazzes.org version0.tar.bz2.