This issue was recorded, reproduced, and apparently fixed for goal 7.1.
http://netbeans.org/bugzilla/show_bug.cgi?id=202673
In the meantime, after each full load of your site, do a search in the console window of the remote log for the command DELE(match case, whole word). This will determine for you which files were deleted, and you can re-upload them.
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