Good news everyone, I got the phone working again!
Turns out I was using old version of zypper (zypper-1.14.6+git4-1.4.1.jolla.armv7hl and augeas-libs-1.6.0+git1-1.2.9.jolla.armv7hl) because I had those files alreayd laying around. As soon as I downloaded and installed new version (zypper-1.14.6+git4-1.5.1.jolla.armv7hl and augeas-libs-1.12.0+git2-1.5.1.jolla.armv7hl) zypper started working.
Next I took few steps from TJC-thread at https://together.jolla.com/question/224620/xperia-x-rokua-update-failed-stuck-in-airplane-mode-after-reboot-selfanswered/?answer=224659#post-id-224659 on how to link the .pk-zypp-dist-upgrade-cache somewhere where zypper can find them and did the dist-upgrade (you probably don’t need the zypper up -command):
mv /var/cache/zypp /var/cache/zypp-old
ln -s /home/.pk-zypp-dist-upgrade-cache /var/cache/zypp
su
zypper up
zypper dup
and after crossing my ringers and knocking on the wood (literally for both), I rebooted the phone and it started normally to my relief.
Of course my first actions were to turn on WLAN and remote access for developer mode 
Then I went to Terminal and and checked the pkcon worked with pkcon refresh and pkcon update and final check of version --dup before finally entering my SIM card from my old JP-1301 (which I had been using for the past 3 days, still works just fine btw.) and rebooted the phone to make sure it still works.
I haven’t noticed anything unusual so far, and I hope this experience reminds me to make my backups in time and make sure I have WLAN and remote access for developer mode enabled before doing next update…