Whole site crashed after creating a new subsite with New Blog Templates

My site (multisite network) has just crashed after my coworker created a new site using New Blog Templates.

- We changed the url of our templates a few days ago.
- When looking inside templates, we saw that pictures inside pages still used the old template url. Pictures were displaying correctly but we were surprised about that.
- This morning, my coworker decided to fix these url. He made a test first with one template. He changed the url directly in text.
- Then he created a new site using this template to see if all works ok.
- It looked ok at first but then the server crashed.

The error log I see is the following:

[Mon Jan 13 09:25:29 2014] [warn] [client 81.220.114.17] mod_fcgid: stderr: Erreur de la base de donn\xc3\xa9es WordPress Table 'monsitedentiste.msd_mcc_nbt_relationship' doesn't exist pour la requ\xc3\xaate DELETE FROM msd_mcc_nbt_relationship WHERE  blog_id = 0 faite par validate_another_blog_signup, wpmu_create_blog, do_action('wpmu_new_blog'), call_user_func_array, default_theme_switch_theme, switch_theme, do_action('switch_theme'), call_user_func_array, MCC_NBT_Integrator->delete_blog_relationships_on_switch_theme, Multisite_Content_Copier_NBT_Model->delete_relationships, referer: http://monsitedentiste.com/wp-signup.php
[Mon Jan 13 09:25:29 2014] [warn] [client 81.220.114.17] mod_fcgid: stderr: Erreur de la base de donn\xc3\xa9es WordPress Duplicate entry '2' for key 'PRIMARY' pour la requ\xc3\xaate INSERT INTO <code>msd_164_terms</code> (<code>term_id</code>,<code>name</code>,<code>slug</code>,<code>term_group</code>) VALUES (2,'Principal','principal',0) faite par validate_another_blog_signup, wpmu_create_blog, do_action('wpmu_new_blog'), call_user_func_array, blog_templates->set_blog_defaults, NBT_Template_copier->execute, call_user_func, NBT_Template_copier->copy_menus, NBT_Template_copier->copy_menu, referer: http://monsitedentiste.com/wp-signup.php
[Mon Jan 13 09:25:29 2014] [warn] [client 81.220.114.17] mod_fcgid: stderr: Erreur de la base de donn\xc3\xa9es WordPress Duplicate entry '2' for key 'PRIMARY' pour la requ\xc3\xaate INSERT INTO <code>msd_164_term_taxonomy</code> (<code>term_taxonomy_id</code>,<code>term_id</code>,<code>taxonomy</code>,<code>description</code>,<code>parent</code>,<code>count</code>) VALUES (2,2,'nav_menu',0,0,7) faite par validate_another_blog_signup, wpmu_create_blog, do_action('wpmu_new_blog'), call_user_func_array, blog_templates->set_blog_defaults, NBT_Template_copier->execute, call_user_func, NBT_Template_copier->copy_menus, NBT_Template_copier->copy_menu, referer: http://monsitedentiste.com/wp-signup.php
[Mon Jan 13 09:25:29 2014] [warn] [client 81.220.114.17] mod_fcgid: stderr: Erreur de la base de donn\xc3\xa9es WordPress Duplicate entry '17-2' for key 'PRIMARY' pour la requ\xc3\xaate INSERT INTO <code>msd_164_term_relationships</code> (<code>object_id</code>,<code>term_taxonomy_id</code>,<code>term_order</code>) VALUES (17,2,0) faite par validate_another_blog_signup, wpmu_create_blog, do_action('wpmu_new_blog'), call_user_func_array, blog_templates->set_blog_defaults, NBT_Template_copier->execute, call_user_func, NBT_Template_copier->copy_menus, NBT_Template_copier->copy_menu, referer: http://monsitedentiste.com/wp-signup.php
[Mon Jan 13 09:25:29 2014] [warn] [client 81.220.114.17] mod_fcgid: stderr: Erreur de la base de donn\xc3\xa9es WordPress Duplicate entry '549-2' for key 'PRIMARY' pour la requ\xc3\xaate INSERT INTO <code>msd_164_term_relationships</code> (<code>object_id</code>,<code>term_taxonomy_id</code>,<code>term_order</code>) VALUES (549,2,0) faite par validate_another_blog_signup, wpmu_create_blog, do_action('wpmu_new_blog'), call_user_func_array, blog_templates->set_blog_defaults, NBT_Template_copier->execute, call_user_func, NBT_Template_copier->copy_menus, NBT_Template_copier->copy_menu, referer: http://monsitedentiste.com/wp-signup.php
[Mon Jan 13 09:25:29 2014] [warn] [client 81.220.114.17] mod_fcgid: stderr: Erreur de la base de donn\xc3\xa9es WordPress Duplicate entry '19-2' for key 'PRIMARY' pour la requ\xc3\xaate INSERT INTO <code>msd_164_term_relationships</code> (<code>object_id</code>,<code>term_taxonomy_id</code>,<code>term_order</code>) VALUES (19,2,0) faite par validate_another_blog_signup, wpmu_create_blog, do_action('wpmu_new_blog'), call_user_func_array, blog_templates->set_blog_defaults, NBT_Template_copier->execute, call_user_func, NBT_Template_copier->copy_menus, NBT_Template_copier->copy_menu, referer: http://monsitedentiste.com/wp-signup.php
[Mon Jan 13 09:25:29 2014] [warn] [client 81.220.114.17] mod_fcgid: stderr: Erreur de la base de donn\xc3\xa9es WordPress Duplicate entry '20-2' for key 'PRIMARY' pour la requ\xc3\xaate INSERT INTO <code>msd_164_term_relationships</code> (<code>object_id</code>,<code>term_taxonomy_id</code>,<code>term_order</code>) VALUES (20,2,0) faite par validate_another_blog_signup, wpmu_create_blog, do_action('wpmu_new_blog'), call_user_func_array, blog_templates->set_blog_defaults, NBT_Template_copier->execute, call_user_func, NBT_Template_copier->copy_menus, NBT_Template_copier->copy_menu, referer: http://monsitedentiste.com/wp-signup.php
[Mon Jan 13 09:25:29 2014] [warn] [client 81.220.114.17] mod_fcgid: stderr: Erreur de la base de donn\xc3\xa9es WordPress Duplicate entry '172-2' for key 'PRIMARY' pour la requ\xc3\xaate INSERT INTO <code>msd_164_term_relationships</code> (<code>object_id</code>,<code>term_taxonomy_id</code>,<code>term_order</code>) VALUES (172,2,0) faite par validate_another_blog_signup, wpmu_create_blog, do_action('wpmu_new_blog'), call_user_func_array, blog_templates->set_blog_defaults, NBT_Template_copier->execute, call_user_func, NBT_Template_copier->copy_menus, NBT_Template_copier->copy_menu, referer: http://monsitedentiste.com/wp-signup.php
[Mon Jan 13 09:25:29 2014] [warn] [client 81.220.114.17] mod_fcgid: stderr: Erreur de la base de donn\xc3\xa9es WordPress Duplicate entry '175-2' for key 'PRIMARY' pour la requ\xc3\xaate INSERT INTO <code>msd_164_term_relationships</code> (<code>object_id</code>,<code>term_taxonomy_id</code>,<code>term_order</code>) VALUES (175,2,0) faite par validate_another_blog_signup, wpmu_create_blog, do_action('wpmu_new_blog'), call_user_func_array, blog_templates->set_blog_defaults, NBT_Template_copier->execute, call_user_func, NBT_Template_copier->copy_menus, NBT_Template_copier->copy_menu, referer: http://monsitedentiste.com/wp-signup.php
[Mon Jan 13 09:25:29 2014] [warn] [client 81.220.114.17] mod_fcgid: stderr: Erreur de la base de donn\xc3\xa9es WordPress Duplicate entry '559-2' for key 'PRIMARY' pour la requ\xc3\xaate INSERT INTO <code>msd_164_term_relationships</code> (<code>object_id</code>,<code>term_taxonomy_id</code>,<code>term_order</code>) VALUES (559,2,0) faite par validate_another_blog_signup, wpmu_create_blog, do_action('wpmu_new_blog'), call_user_func_array, blog_templates->set_blog_defaults, NBT_Template_copier->execute, call_user_func, NBT_Template_copier->copy_menus, NBT_Template_copier->copy_menu, referer: http://monsitedentiste.com/wp-signup.php

Because of that, my whole VPS is down ("error establishing a database connection").

Best Regards