Milev

Now I have done everything as you said and indeed user sites appeared. I have prepared fresh wp-admin folder just with config files, plugins and default themes. When everything was ready (plugins off, default theme) I just switched the folders and Sites were there again. Looks like some extra code cleaning awaits!

Just needed somebody to force me to do those steps as the system is complex. 😉
Thank you!

1
The changes are short, and easy to find by first line.

1.1
wp­-admin/update-­core.php

function core_upgrade_preamble() {
    return; //here

1.2
wp­-admin/network/update­-core.php

/** Load WordPress Administration Bootstrap */
require_once( './admin.php' );
wp_die( "No update allowed"); //here

1.3
wp­-admin/network/site­-users.php
original:

// If the user doesn't already belong to the blog, bail.
if ( !is_user_member_of_blog($user_id ) )
wp_die(__( 'Cheatin’ uh?' ) );

changed:

var_dump(is_user_member_of_blog($user_id ));

1.4
wp-admin/themes.php
here is a big redesign with roles and this kind of stuff.
=====
Have I blocked some part of DB update keeping changes in those files?
Just in case I’ll make network update without that changes.

2
It’s just made with db-config.php file required in wp-config.php. Then blogs are spread by id to differend DBs. I don’t think that is the source of problem. At least not the first one to check.

3
Sample rows from wp_usermeta for one of users are:
(umeta_id, user_id, meta_key, meta_value)

(78185, 3838, 'first_name', 'aaa'),
(78186, 3838, 'last_name', 'bbb'),
(78187, 3838, 'nickname', 'ccc'),
(78188, 3838, 'description', ''),
(78189, 3838, 'rich_editing', 'true'),
(78190, 3838, 'comment_shortcuts', 'false'),
(78191, 3838, 'admin_color', 'fresh'),
(78192, 3838, 'use_ssl', '0'),
(78193, 3838, 'show_admin_bar_front', 'true'),
(78201, 3838, 'wp_2987_capabilities', 'a:1:{s:13:"administrator";s:1:"1";}'),
(78195, 3838, 'wp_1_user_level', '0'),
(78196, 3838, 'aim', ''),
(78197, 3838, 'yim', ''),
(78198, 3838, 'jabber', ''),
(78199, 3838, 'primary_blog', '2987'),
(78200, 3838, 'show_welcome_panel', '0'),
(78202, 3838, 'wp_2987_user_level', '10'),
(78203, 3838, 'wp_2987_dashboard_quick_press_last_post_id', '52'),
(78222, 3838, 'managenav-menuscolumnshidden', 'a:4:{i:0;s:11:"link-target";i:1;s:11:"css-classes";i:2;s:3:"xfn";i:3;s:11:"description";}'),
(78223, 3838, 'metaboxhidden_nav-menus', 'a:2:{i:0;s:8:"add-post";i:1;s:12:"add-post_tag";}'),
(78234, 3838, 'dismissed_wp_pointers', 'wp330_media_uploader,wp330_toolbar'),
(78235, 3838, 'wp_2987_user-settings', 'galfile=1&galord=title&editor=tinymce'),
(78236, 3838, 'wp_2987_user-settings-time', '1339779759'),
(78237, 3838, 'nav_menu_recently_edited', '613');
(78238, 3838, 'closedpostboxes_nav-menus', 'a:1:{i:0;s:8:"add-page";}'),

4
By the way /wp-admin/network/site-users.php?id= works fine and shows users for given id number.