in the current trunk version lyx asks twice if it should overwrite a file when 
saving.

The reason is that the qt save dialog asks and lyx itself asks too. The qt part can easily be turned off by the attached patch.

Bernhard
Index: src/frontends/qt4/FileDialog.C
===================================================================
--- src/frontends/qt4/FileDialog.C      (revision 16889)
+++ src/frontends/qt4/FileDialog.C      (working copy)
@@ -91,6 +91,7 @@
        LyXFileDialog dlg(title_, path, filters, private_->b1, private_->b2);
        dlg.setFileMode(QFileDialog::AnyFile);
        dlg.setAcceptMode(QFileDialog::AcceptSave);
+       dlg.setConfirmOverwrite(false);
 
        if (!suggested.empty())
                dlg.selectFile(toqstr(suggested));

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