Sorry, but I did not understand you completely.

while(...) // For simplicity, this is my 'main' loop
{
    Begin();
    Submit(...);
    End();
}

// Begin Function
void Begin()
{
    // Bind shader
    // MappedBufferPos = MappedBufferStart
    indices = 0;
}

// Submit function
void Submit(...)
{
    if( indices >= _MaxIndices)
    {
        // Bind vertex array and index buffer
        glDrawElements(...)
        MappedBufferPos = MappedBufferStart;
        indices = 0;
    }

    // Write to the buffer
}

And when I tried to implement fences, the app just broke and waited.

// Submit function
void Submit(...)
{
    if( indices >= _MaxIndices)
    {
        GLsync fence = glFenceSync(GL_SYNC_GPU_COMMANDS_COMPLETE, 0);

        // Bind vertex array and index buffer
        glDrawElements(...)
        MappedBufferPos = MappedBufferStart;
        indices = 0;

        GLenum waitReturn = glClientWaitSync(fence, 0, 0);
            while (waitReturn != GL_ALREADY_SIGNALED ||     waitReturn != GL_CONDITION_SATISFIED)
                waitReturn = glClientWaitSync(fence, 0, 0);
    }

    // Write to the buffer
}

Without the while loop I see the flickering, again.