After looking at the logs, I cannot explain why it went wrong on the second wiki 
Good news is that your first Wiki is fine and it can be backuped correctly as the script ‘backup’ is fine now.
My troubleshooting went like this:
In the php logs, we have this
[09-Nov-2018 11:20:40] ERROR: An another FPM instance seems to already listen on /var/run/php/php7.0-fpm-dokuwiki.sock
[09-Nov-2018 11:20:40] ERROR: An another FPM instance seems to already listen on /var/run/php/php7.0-fpm-dokuwiki.sock
[09-Nov-2018 11:20:40] ERROR: FPM initialization failed
[09-Nov-2018 11:20:40] ERROR: FPM initialization failed
[09-Nov-2018 13:11:52] ERROR: [pool dokuwiki__2] the chdir path '/var/www/dokuwiki__2' does not exist or is not a directory
[09-Nov-2018 13:11:52] ERROR: failed to post process the configuration
[09-Nov-2018 13:11:52] ERROR: FPM initialization failed
[09-Nov-2018 13:55:59] NOTICE: fpm is running, pid 6764
[09-Nov-2018 13:55:59] NOTICE: ready to handle connections
The file you had to remove can be seen but is is not the root cause of the issue
[09-Nov-2018 13:11:52] ERROR: [pool dokuwiki__2] the chdir path '/var/www/dokuwiki__2' does not exist or is not a directory
It was left by the removal script and it is due to a bug that have been patched by the last Yunohost 3.3.1 (see at the end of the post)
The logs at 11:20 are more interesting and show why php failed to restart. And lead Yunohost to remove then restore your (faulty backuped) data
I cannot explain the failure because both installation used the same helper ynh_add_fpm_config to handle the php configuration.
I leave this into the hands of @Apps people if they have time and energy to look at this. I do not know where to search next.
Continuing the discussion from YunoHost 3.3 release / Sortie de YunoHost 3.3: