I have programmer laying around here somewhere but I’ll try it this way first 
Allright, I changed the const byte min_pulsewidth to 0 and copied the src.ino.atmega328p-xmini.hex file to the Rpi as latest.hex under /home/pi/emonpi/firmware/compiled/
Stopped emonhub, ran the avrdude cmd, started emonhub. I got the following with a couple of broken pipes but it seemed to work.
avrdude-original: Version 6.3-20171130
Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
Copyright (c) 2007-2014 Joerg Wunsch
              System wide configuration file is "/etc/avrdude.conf"
              User configuration file is "/root/.avrduderc"
              User configuration file does not exist or is not a regular file, skipping
              Using Port                    : /dev/ttyAMA0
              Using Programmer              : arduino
              Overriding Baud Rate          : 115200
avrdude-original: Using autoreset DTR on GPIO Pin 7
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
                flash         65     6   128    0 yes     32768  128    256  4500  4500 0xff 0xff
                lfuse          0     0     0    0 no          1    0      0  4500  4500 0x00 0x00
                hfuse          0     0     0    0 no          1    0      0  4500  4500 0x00 0x00
                efuse          0     0     0    0 no          1    0      0  4500  4500 0x00 0x00
                lock           0     0     0    0 no          1    0      0  4500  4500 0x00 0x00
                calibration    0     0     0    0 no          1    0      0     0     0 0x00 0x00
                signature      0     0     0    0 no          3    0      0     0     0 0x00 0x00
              Programmer Type : Arduino
              Description     : Arduino
              Hardware Version: 3
              Firmware Version: 4.4
              Vtarget         : 0.3 V
              Varef           : 0.3 V
              Oscillator      : 28.800 kHz
              SCK period      : 3.3 us
avrdude-original: AVR device initialized and ready to accept instructions
Reading | ################################################## | 100% 0.00s
avrdude-original: Device signature = 0x1e950f (probably m328p)
avrdude-original: safemode: lfuse reads as 0
avrdude-original: safemode: hfuse reads as 0
avrdude-original: safemode: efuse reads as 0
avrdude-original: NOTE: “flash” memory has been specified, an erase cycle will be performed
To disable this feature, specify the -D option.
avrdude-original: erasing chip
avrdude-original: reading input file “/home/pi/emonpi/firmware/compiled/latest.hex”
avrdude-original: input file /home/pi/emonpi/firmware/compiled/latest.hex auto detected as Intel Hex
avrdude-original: writing flash (18356 bytes):
Writing | ################################################## | 100% 2.57s
avrdude-original: 18356 bytes of flash written
avrdude-original: verifying flash memory against /home/pi/emonpi/firmware/compiled/latest.hex:
avrdude-original: load data flash data from input file /home/pi/emonpi/firmware/compiled/latest.hex:
avrdude-original: input file /home/pi/emonpi/firmware/compiled/latest.hex auto detected as Intel Hex
avrdude-original: input file /home/pi/emonpi/firmware/compiled/latest.hex contains 18356 bytes
avrdude-original: reading on-chip flash data:
Reading | ################################################## | 100% 1.98s
avrdude-original: verifying …
avrdude-original: 18356 bytes of flash verified
avrdude-original: safemode: lfuse reads as 0
avrdude-original: safemode: hfuse reads as 0
avrdude-original: safemode: efuse reads as 0
avrdude-original: safemode: Fuses OK (E:00, H:00, L:00)
strace: |autoreset: Broken pipe
strace: |autoreset: Broken pipe
strace: |autoreset: Broken pipe
strace: |autoreset: Broken pipe
strace: |autoreset: Broken pipe
avrdude-original done.  Thank you.
strace: |autoreset: Broken pipe
The webinterface showed everything in order. And yessss, the pulse counter can now keep up with the real usage. A waterkettle, portable roomheater and all four of the ceramic stove pits on full will easily go to 10kW which is now perfectly showing up on the emonPi.
Robert, thx for all the quick replies and solution!