Well, after I deleted all entries in vhosts_bootstrap.conf, I also deleted all folders from /etc/apache2/plesk.conf.d/vhosts/ where were all the subdomains conf files (sub1.domain.com, sub2.domain.com), from subscription previously deleted.
(I've deleted subscription eg.: domain.com
Under this subscription there were few subdomains: sub1.domain.com, sub2.domain.com etc...)
So after I deleted a subscription and tried to --reconfigure-all I had error "..... bad user name wyderka" etc. shown abowe.
Then I've deleted all entries from bootstrap and from folder. I do not know what exactly was the problem but after this I was able to reconfigure-all with no errors and all my sites work fine.
sorry for the grammar ;-)