So after a lot of digging I found out that now one should update all of the config files used for netatalk before (/etc/netatalk/afpd.conf, /etc/netatalk/AppleVolumes.default, /etc/netatalk/netatalk.conf) to the new Netatalk 3.0 config file which consists of only ONE file called afp.conf in /etc/.
So to sum up and cut the cr4p, if you setup your time machine with the guide in the ArchlinuxArm site this is how to get it back and working:
1) $this->bbcode_second_pass_code('', '# mv /etc/netatalk/afppasswd /etc/')
2) open each of these files $this->bbcode_second_pass_code('', '/etc/netatalk/afpd.conf, /etc/netatalk/AppleVolumes.default, /etc/netatalk/netatalk.conf') and copy the content somewhere that you can have it opened next to the terminal window
3) $this->bbcode_second_pass_code('', '# nano /etc/afp.conf')
4) Use this to find the equivalents for your configs:
http://netatalk.sourceforge.net/3.0/htmldocs/upgrade.html#id42830345) Ctrl + X then Y and then Enter
6) Make sure you have $this->bbcode_second_pass_code('', '/etc/avahi/services/afpd.service') if you don't follow the guide in
http://archlinuxarm.org/support/guides/applications/time-machine ONLY FOR THAT SPECIFIC FILE (in my case, it got removed by the avahi update when netatalk was updated too).
7) $this->bbcode_second_pass_code('', '# /etc/rc.d/netatalk restart && /etc/rc.d/avahi-daemon restart')
8) Your done, enjoy!
I hope this avoids some of you the trouble of loosing hours of sleep as I have tonight.
Just as an example I'm pasting my finished updated version of /etc/afp.conf (again, this is now the only netatalk conf file. This 3: /etc/netatalk/afpd.conf, /etc/netatalk/AppleVolumes.default, /etc/netatalk/netatalk.conf are now obsolete and not used anymore which is why all of the AFP shares stopped working after the update).
$this->bbcode_second_pass_code('', '
;
; Netatalk 3.x configuration file
;
[Global]
; Global server settings
;Start updated AFPD.CONF
mimic model = Macmini
uam list = uams_dhx2.so
; Start updated netatalk update manually done from old /etc/netatalk/netatlak.conf
unix charset = UTF8
mac charset = MAC_ROMAN
max connections = 50
; [Homes]
; basedir regex = /xxxx
; [My AFP Volume]
; path = /path/to/volume
; Start updated AppleVolume.defaults
[TimeMachine]
path = /media/Chronos/timemachine
time machine = yes
[Musica]
path = /media/FreeAgent_GoFlex_Drive/Musica
[Pelis]
path = /media/FreeAgent_GoFlex_Drive/Pelis
[Software]
path = /media/FreeAgent_GoFlex_Drive/Software
[BitTorrents Downloads]
path = /media/FreeAgent_GoFlex_Drive/BitTorrents
[TV Series]
path = /media/FreeAgent_GoFlex_Drive/TV_Series
')