1. First double check the solder joints of the 40-pin Header of the FabScanPi-HAT. If you are sure that there are no 'cold' solder joints move on reading, otherwise resolder those joints. Try again and have a look to the logs. If the error still occurs continue reading with 3.
2. Check if your fabscanpi-server version is 0.8.0 or higher. Have a look into your default.config.json and check the serial baudrate. It should be 57600 for fabscanpi-server >= 0.4.2. If you changed the baudrate and the error still occurs continue with reading 3.
3. Your bootloader is bricked, what means that you need to flash a new bootloader to your FabScanPi HAT. Continue with reading "How to flash the FabScanPi HAT Bootloader?"

How to flash the Bootloader?

! If you want to leave the HAT connected to the pi during the flashing process. Be sure you stopped the FabScanPi Server. You can use the following command to do that. !

$ sudo /etc/init.d/fabscanpi-server stop 

Option A: Using Raspberry Pi for flashing.

Connect the FabScanPi HAT pins as described below. (solder some wires to the solder pads). Use a resistor 2k2...5k6 in series for every signal. (see picture for details)

RPi  -> Target
IO25 -> Reset
IO11 -> SCK
IO10 -> MOSI
IO9  -> MISO
GND  -> GND

Download bootloader:

$ wget https://github.com/watterott/RPi-UNO-HAT/raw/master/docs/bloader.hex 

Edit the file avrdude.conf  and add the following lines:

$ sudo nano /usr/local/etc/avrdude.conf 
programmer id = "pi_isp"; 
 desc = "GPIO bitbang"; 
 type = "linuxgpio";   
 reset = 25; sck = 11;
 mosi = 10; 
 miso = 9;
;

Flash bootloader:

$ avrdude -c pi_isp -p m328p -e -U flash:w:bloader.hex:i -U lfuse:w:0xFF:m -U hfuse:w:0xD6:m -U efuse:w:0x05:m -U lock:w:0x0F:m

Option B: Using Arduino Uno (device ttyACM0 or ttyUSB0 ) for flashing.

Connection (Arduino Uno connected to RPi via USB):

Uno -> Target 
D10 -> Reset 
D13 -> SCK 
D11 -> MOSI 
D12 -> MISO 
GND -> GND

Download bootloader and ISP firmware:

$ wget https://raw.githubusercontent.com/watterott/RPi-UNO-HAT/master/software/bloader.hex
$ wget https://raw.githubusercontent.com/watterott/RPi-UNO-HAT/master/software/isp.hex 

Flash ISP firmware to Arduino Uno:

 $ avrdude -c arduino -P /dev/ttyUSB0 -b 115200 -p m328p -e -U flash:w:isp.hex:i 

or

 $ avrdude -c arduino -P /dev/ttyACM0 -b 115200 -p m328p -e -U flash:w:isp.hex:i 

Flash bootloader:

$ avrdude -c stk500v1 -P /dev/ttyUSB0 -b 19200 -p m328p -e -U flash:w:bloader.hex:i -U lfuse:w:0xFF:m -U hfuse:w:0xD6:m -U efuse:w:0x05:m -U lock:w:0x0F:m

or

$ avrdude -c stk500v1 -P /dev/ttyACM0 -b 19200 -p m328p -e -U flash:w:bloader.hex:i -U lfuse:w:0xFF:m -U hfuse:w:0xD6:m -U efuse:w:0x05:m -U lock:w:0x0F:m