Problem uploading firmware to ATmega328 (8-Bit board)

I' m trying to make changes to the firmware of the ATmega328 on the 8-Bit board.
When starting the upload, avrdude is sending and receiving a couple of data.
But finally it always ends at the same point (see below) with the following error:

avrdude: ser_recv(): programmer is not responding
avrdude: stk500_recv(): programmer is not responding
Problem uploading to board.

The original board firmware is dead now.
No status information from the µC is coming any more. And of course no streaming data.

Programming the RFDuinos is working fine.

I tried using Arduino 1.6.5 as well as 1.5.8
In 1.6.5 I selected "Arduino/Genuino Uno"
In 1.5.8 "Arduino Uno"

I tried everything mentioned in the troubleshooting including increment the pollTime of the RFDuino device from 50 to 80 in 5er increments.
As well I minimized the code trying to upload, to get rid of the "low memory" warning. But it resulted in the same error at the end.

Any hints what I can do to get the ATmega running again?
How can I check whether the bootloader is working well?

Board: OpenBCI v3-8
Firmware: Board: OpenBCI_8bit
                 Radio: Ver_1xx_2014-Fall2016

Any hints are appreciated.
Thanks a lot,
Bernd


Following is the output when uploading with 1.5.8
Using 1.6.5 is similar but less detailed (missing Send:, Recv: infos)

Build options changed, rebuilding all

Sketch uses 23,620 bytes (73%) of program storage space. Maximum is 32,256 bytes.
Global variables use 1,540 bytes (75%) of dynamic memory, leaving 508 bytes for local variables. Maximum is 2,048 bytes.
Low memory available, stability problems may occur.
C:\Program Files\Arduino_1.5.8/hardware/tools/avr/bin/avrdude -CC:\Program Files\Arduino_1.5.8/hardware/tools/avr/etc/avrdude.conf -v -v -v -v -patmega328p -carduino -PCOM6 -b115200 -D -Uflash:w:C:\Users\battes\AppData\Local\Temp\build5031677044257408213.tmp/OpenBCI_8bit_BLE.cpp.hex:i

avrdude: Version 6.0.1, compiled on Apr  3 2014 at 23:12:16
         Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
         Copyright (c) 2007-2009 Joerg Wunsch

         System wide configuration file is "C:\Program Files\Arduino_1.5.8/hardware/tools/avr/etc/avrdude.conf"

         Using Port                    : COM6
         Using Programmer              : arduino
         Overriding Baud Rate          : 115200
avrdude: Send: 0 [30]   [20]
avrdude: Send: 0 [30]   [20]
avrdude: Send: 0 [30]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [10]
         AVR Part                      : ATmega328P
         Chip Erase delay              : 9000 us
         PAGEL                         : PD7
         BS2                           : PC2
         RESET disposition             : dedicated
         RETRY pulse                   : SCK
         serial program mode           : yes
         parallel program mode         : yes
         Timeout                       : 200
         StabDelay                     : 100
         CmdexeDelay                   : 25
         SyncLoops                     : 32
         ByteDelay                     : 0
         PollIndex                     : 3
         PollValue                     : 0x53
         Memory Detail                 :

                                  Block Poll               Page                       Polled
           Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
           ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
           eeprom        65    20     4    0 no       1024    4      0  3600  3600 0xff 0xff
                                  Block Poll               Page                       Polled
           Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
           ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
           flash         65     6   128    0 yes     32768  128    256  4500  4500 0xff 0xff
                                  Block Poll               Page                       Polled
           Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
           ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
           lfuse          0     0     0    0 no          1    0      0  4500  4500 0x00 0x00
                                  Block Poll               Page                       Polled
           Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
           ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
           hfuse          0     0     0    0 no          1    0      0  4500  4500 0x00 0x00
                                  Block Poll               Page                       Polled
           Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
           ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
           efuse          0     0     0    0 no          1    0      0  4500  4500 0x00 0x00
                                  Block Poll               Page                       Polled
           Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
           ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
           lock           0     0     0    0 no          1    0      0  4500  4500 0x00 0x00
                                  Block Poll               Page                       Polled
           Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
           ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
           calibration    0     0     0    0 no          1    0      0     0     0 0x00 0x00
                                  Block Poll               Page                       Polled
           Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
           ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
           signature      0     0     0    0 no          3    0      0     0     0 0x00 0x00

         Programmer Type : Arduino
         Description     : Arduino
avrdude: Send: A [41] . [80]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [03]
avrdude: Recv: . [10]
avrdude: Send: A [41] . [81]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [04]
avrdude: Recv: . [10]
avrdude: Send: A [41] . [82]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [04]
avrdude: Recv: . [10]
avrdude: Send: A [41] . [98]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [03]
avrdude: Recv: . [10]
         Hardware Version: 3
         Firmware Version: 4.4
avrdude: Send: A [41] . [84]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [03]
avrdude: Recv: . [10]
avrdude: Send: A [41] . [85]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [03]
avrdude: Recv: . [10]
avrdude: Send: A [41] . [86]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [03]
avrdude: Recv: . [10]
avrdude: Send: A [41] . [87]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [03]
avrdude: Recv: . [10]
avrdude: Send: A [41] . [89]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [03]
avrdude: Recv: . [10]
         Vtarget         : 0.3 V
         Varef           : 0.3 V
         Oscillator      : 28.800 kHz
         SCK period      : 3.3 us

avrdude: Send: A [41] . [81]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [04]
avrdude: Recv: . [10]
avrdude: Send: A [41] . [82]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [04]
avrdude: Recv: . [10]
avrdude: Send: B [42] . [86] . [00] . [00] . [01] . [01] . [01] . [01] . [03] . [ff] . [ff] . [ff] . [ff] . [00] . [80] . [04] . [00] . [00] . [00] . [80] . [00]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [10]
avrdude: Send: E [45] . [05] . [04] . [d7] . [c2] . [00]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [10]
avrdude: Send: P [50]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [10]
avrdude: AVR device initialized and ready to accept instructions

Reading | avrdude: Send: u [75]   [20]
avrdude: Recv: . [14] . [1e] . [95] . [0f] . [10]
################################################## | 100% 0.13s

avrdude: Device signature = 0x1e950f
avrdude: reading input file "C:\Users\battes\AppData\Local\Temp\build5031677044257408213.tmp/OpenBCI_8bit_BLE.cpp.hex"
avrdude: writing flash (23620 bytes):

Writing | avrdude: Send: U [55] . [00] . [00]   [20]
avrdude: Recv: . [14]
avrdude: Recv: . [10]
avrdude: Send: d [64] . [00] . [80] F [46] . [0c] . [94] . [e8] . [02] . [0c] . [94] . [10] . [03] . [0c] . [94] . [10] . [03] . [0c] . [94] . [10] . [03] . [0c] . [94] . [10] . [03] . [0c] . [94] . [10] . [03] . [0c] . [94] . [10] . [03] . [0c] . [94] . [10] . [03] . [0c] . [94] . [10] . [03] . [0c] . [94] . [10] . [03] . [0c] . [94] . [10] . [03] . [0c] . [94] . [10] . [03] . [0c] . [94] . [10] . [03] . [0c] . [94] . [10] . [03] . [0c] . [94] . [10] . [03] . [0c] . [94] . [10] . [03] . [0c] . [94] . [16] ( [28] . [0c] . [94] . [10] . [03] . [0c] . [94] . [04] + [2b] . [0c] . [94] 6 [36] + [2b] . [0c] . [94] . [10] . [03] . [0c] . [94] . [10] . [03] . [0c] . [94] . [10] . [03] . [0c] . [94] . [10] . [03] . [0c] . [94] . [10] . [03] . [0c] . [94] . [10] . [03] . [e3] . [0a] . [93] . [0b] . [eb] . [0a] . [f0] . [0a] . [f5] . [0a] . [ff] . [0a] . [93] . [0b] . [93] . [0b] . [93] . [0b] . [04] . [0b] . [93] . [0b] . [93] . [0b]   [20]
avrdude: ser_recv(): programmer is not responding
avrdude: stk500_recv(): programmer is not responding
Problem uploading to board.  See http://www.arduino.cc/en/Guide/Troubleshooting#upload for suggestions.