I don't use any code repository tools myself but I'd be very surprised if
the Eclipse was somehow deleting source code from your repository upon doing
a build. I can't imagine why it would do so. Isn't the whole idea of a
repository to *save* each version of the source code? What repository are
you using? CVS? SVN?

Also, I'm not clear why you can't access the newsgroups on the eclipse.org
news server; I think they are clearly the best place to ask this kind of
question. All you need to know is the "secret" password for the news
server - which hasn't changed in the four years that I've been using
Eclipse - and you should be able to post there. The newsgroups there are
very active and focused entirely on Eclipse issues.

As for the automatic build option, I believe that Eclipse's default
behaviour is to rebuild every project in Eclipse every time you save
something; that's not as big a deal as it first sounds because of the
incremental compiles that it does. You can disable this automatic build by
going to the Project menu on the main toolbar and unchecking "Build
automatically" if it is currently checked. That will activate some other
options that are normally greyed out, including Build All and Build Project.
That enables you to build when _you_ want to, not when Eclipse wants to.

--
Rhino

If Eclipse is deleting something occasionally when building, chances are
you've configured that location as its output directory.  In that case,
you've seriously hosed your project configuration.  Do NOT follow the
instructions you got elsewhere.  Leaving Eclipse poised to delete your
source code if you forget a step is about the worst idea I've ever seen.

Instead, right-click the project, choose "Properties", and then in the
"Java Build Path" section, move the output directory to the right place.  
Typically, by the way, your source code repository should not even be in
your project folder at all!