How to read from multiple channels of the ADC on an STM32F407?
hadc1.Init.ScanConvMode = DISABLE;


the sequencer is disabled so you cant read or even convert data coming from the other channel.
Also you have to define the rank of every channel. 
for exemple :

sConfig.Rank      = 1;
     sConfig.SamplingTime = ADC_SAMPLETIME_1CYCLE_5 ;
     sConfig.Channel = REF_1_5_Volt_Pin;
     HAL_ADC_ConfigChannel(&amp;hadc, &amp;sConfig);
 sConfig.Rank = 2;
 sConfig.Channel = L1_voltage_Pin;
 HAL_ADC_ConfigChannel(&amp;hadc, &amp;sConfig);

 sConfig.Rank = 3;
 sConfig.Channel = L2_voltage_Pin;
 HAL_ADC_ConfigChannel(&amp;hadc, &amp;sConfig);

 sConfig.Rank = 4;
 sConfig.Channel = L3_voltage_Pin;
 HAL_ADC_ConfigChannel(&amp;hadc, &amp;sConfig);

 sConfig.Rank = 5;
 sConfig.Channel = L1_curent_Pin;
 HAL_ADC_ConfigChannel(&amp;hadc, &amp;sConfig);

 sConfig.Rank = 6;
 sConfig.Channel = L2_curent_Pin;
 HAL_ADC_ConfigChannel(&amp;hadc, &amp;sConfig);

 sConfig.Rank = 7
 sConfig.Channel = L3_curent_Pin;
 HAL_ADC_ConfigChannel(&amp;hadc, &amp;sConfig)