Upgrading to 2.8.29 has removed assets

Hi,

We have recently upgraded a client's site from 2.7.10 to the latest version and in the process lost around 3-4 pages of assets. We hoped this would fix an old error of the resource_log table not existing.

We have managed to restore the files (working locally) and they are appearing in their respective regions, but are still missing from the assets manager. Re-saving the regions has not put them back into the assets manager.

If we set PERCH_CLEAN_RESOURCES to true they are deleted again. Is there a way of returning these files to the asset manager? We have tried the tricks of update/?force=upgrade and /apps/assets/reindex and these have not worked.

Diagnostics report:

Perch: 2.8.29
Production mode: Production (100)
Installed apps: content (2.8.29), assets (2.8.29), categories (2.8.29), perch_blog (4.6), perch_forms (1.8.3)
DB driver: PDO
DB tables: perch2_blog_authors (5), perch2_blog_comments (0), perch2_blog_index (1370), perch2_blog_posts (25), perch2_blog_posts_to_tags (32), perch2_blog_sections (1), perch2_blog_tags (32), perch2_categories (2), perch2_category_counts (2), perch2_category_sets (1), perch2_content_index (6266), perch2_content_items (944), perch2_content_regions (131), perch2_forms (5), perch2_forms_responses (3226), perch2_navigation (0), perch2_navigation_pages (0), perch2_page_templates (31), perch2_pages (47), perch2_resource_log (111), perch2_resource_tags (0), perch2_resources (195), perch2_resources_to_tags (0), perch2_scheduled_tasks (10), perch2_settings (25), perch2_user_passwords (0), perch2_user_privileges (38), perch2_user_role_privileges (30), perch2_user_roles (2), perch2_users (7)
Users: 7
App runtimes:
<?php
    $apps_list = array(
        'content', 
        'categories',
        'perch_blog',
        'perch_forms'
    );
Scheduled tasks for perch_blog: delete_spam_comments (1440 mins)
Editor plug-ins: markitup, redactor
H1: 7a8b3443102233372964d684dbb9f481
L1: 737403f988f52016207ce34dddf84c08
F1: 2edba60ed1f613d6dd804feb202456a2
headerColour: #EB307B
content_singlePageEdit: 0
siteURL: /
hideBranding: 1
content_collapseList: 1
lang: en-gb
update_2.7.10: done
latest_version: 2.8.15
on_sale_version: 2.8.29
headerScheme: dark
dashboard: 0
hide_pwd_reset: 0
content_hideNonEditableRegions: 0
content_frontend_edit: 0
helpURL: https://rootstudio.co.uk
logoPath: /admin/resources/loco-logo.png
perch_blog_update: 5.0
perch_blog_post_url: /about-us/blog/post.php?s={postSlug}
perch_blog_slug_format: %Y-%m-%d-{postTitle}
perch_blog_akismet_key:
perch_blog_max_spam_days: 0
perch_blog_comment_notify: 0
update_2.8.29: done
PERCH_DEVELOPMENT: 10
PERCH_STAGING: 50
PERCH_PRODUCTION: 100
PERCH_TZ: UTC
PERCH_EMAIL_FROM: noreply@loco2energy.com
PERCH_EMAIL_FROM_NAME: LoCO2 Energy
PERCH_LOGINPATH: /admin
PERCH_PATH: /Users/James/Repositories/LoCO2 Energy/loco2-core-site/admin
PERCH_CORE: /Users/James/Repositories/LoCO2 Energy/loco2-core-site/admin/core
PERCH_RESFILEPATH: /Users/James/Repositories/LoCO2 Energy/loco2-core-site/admin/resources
PERCH_RESPATH: /admin/resources
PERCH_HTML5: 1
PERCH_CLEAN_RESOURCES:
PERCH_DB_USERNAME: root
PERCH_DB_SERVER: localhost
PERCH_DB_DATABASE: carbon_perch
PERCH_DB_PREFIX: perch2_
PERCH_DEBUG: 1
PERCH_RUNWAY:
PERCH_ERROR_MODE: DIE
PERCH_DATE_LONG: %d %B %Y
PERCH_DATE_SHORT: %d %b %Y
PERCH_TIME_SHORT: %H:%M
PERCH_TIME_LONG: %H:%M:%S
PERCH_RUNWAY_ROUTED:
PERCH_STRONG_PASSWORDS:
PERCH_PREVIEW_ARG: preview
PERCH_TEMPLATE_PATH: /Users/James/Repositories/LoCO2 Energy/loco2-core-site/admin/templates
PERCH_DEFAULT_DOC: index.php
PERCH_DEFAULT_EXT: .php
PERCH_PRODUCTION_MODE: 100
PERCH_RWD:
PERCH_HTML_ENTITIES:
PERCH_SSL:
PERCH_STRIPSLASHES:
PERCH_PROGRESSIVE_FLUSH: 1
PERCH_PARANOID:
PERCH_FORCE_SECURE_COOKIES:
PERCH_PASSWORD_MIN_LENGTH: 6
PERCH_MAX_FAILED_LOGINS: 10
PERCH_AUTH_LOCKOUT_DURATION: 1 HOUR
PERCH_VERIFY_UPLOADS:
PERCH_AUTH_PLUGIN:
PERCH_DB_CHARSET: utf8
PERCH_DB_PORT:
PERCH_DB_SOCKET:
PERCH_SESSION_TIMEOUT_MINS: 20
HOSTING SETTINGS

PHP: 5.6.10
Zend: 2.6.0
OS: Darwin
SAPI: cgi-fcgi
Safe mode: not detected
MySQL client: mysqlnd 5.0.11-dev - 20120503 - $Id: 3c688b6bbc30d36af3ac34fdd4b7b5b787fe5555 $
MySQL server: 5.5.42
Free disk space: 469.81 GB
Extensions: Core, date, ereg, libxml, openssl, pcre, sqlite3, zlib, bcmath, bz2, calendar, ctype, curl, dom, hash, fileinfo, filter, ftp, gd, SPL, iconv, intl, json, ldap, mbstring, session, standard, mysqlnd, mysqli, PDO, pdo_mysql, pdo_sqlite, Phar, posix, readline, Reflection, mysql, SimpleXML, soap, sockets, exif, tokenizer, wddx, xml, xmlreader, xmlwriter, xsl, zip, cgi-fcgi, imap, gettext, mcrypt, yaz, pgsql, pdo_pgsql, xdebug
GD: Yes
ImageMagick: No
PHP max upload size: 32M
PHP max form post size: 32M
PHP memory limit: 128M
Total max uploadable file size: 32M
Resource folder writeable: Yes
Session timeout: 24 minutes
Native JSON: Yes
Filter functions: Yes
Transliteration functions: Yes
PHP_FCGI_CHILDREN: 4
PWD: /Applications/MAMP/fcgi-bin
PHP_FCGI_MAX_REQUESTS: 200
__CF_USER_TEXT_ENCODING: 0x1F5:0x0:0x0
ORIG_SCRIPT_NAME: /fcgi-bin/php5.6.10.fcgi
ORIG_PATH_TRANSLATED: /Users/James/Repositories/LoCO2 Energy/loco2-core-site/admin/core/settings/diagnostics/index.php
ORIG_PATH_INFO: /admin/core/settings/diagnostics/index.php
ORIG_SCRIPT_FILENAME: /Applications/MAMP/fcgi-bin/php5.6.10.fcgi
SCRIPT_NAME: /admin/core/settings/diagnostics/index.php
REQUEST_URI: /admin/core/settings/diagnostics/?extended
QUERY_STRING: extended
REQUEST_METHOD: GET
SERVER_PROTOCOL: HTTP/1.1
GATEWAY_INTERFACE: CGI/1.1
REDIRECT_URL: /admin/core/settings/diagnostics/index.php
REDIRECT_QUERY_STRING: extended
REMOTE_PORT: 56901
SCRIPT_FILENAME: /Users/James/Repositories/LoCO2 Energy/loco2-core-site/admin/core/settings/diagnostics/index.php
SERVER_ADMIN: you@example.com
DOCUMENT_ROOT: /Users/James/Repositories/LoCO2 Energy/loco2-core-site
REMOTE_ADDR: ::1
SERVER_PORT: 80
SERVER_ADDR: ::1
SERVER_NAME: loco2energy.local
SERVER_SOFTWARE: Apache
PATH: /usr/bin:/bin:/usr/sbin:/sbin
HTTP_ACCEPT_ENCODING: gzip, deflate
HTTP_REFERER: https://loco2energy.local/admin/core/settings/diagnostics/
HTTP_ACCEPT_LANGUAGE: en-us
HTTP_USER_AGENT: Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_4) AppleWebKit/601.5.17 (KHTML, like Gecko) Version/9.1 Safari/601.5.17
HTTP_COOKIE: __ar_v4=TVE67VTYJBEYXFJHCDWVIL%3A20160411%3A64%7CTJITBEHNGNCGDHTCVQNWH3%3A20160411%3A64%7COMJFB4T7FJDTFPE4DEGNKB%3A20160411%3A64; __utma=151388196.944186722.1453973320.1460360090.1460451639.12; __utmb=151388196.54.10.1460451639; __utmc=151388196; __utmz=151388196.1453973320.1.1.utmcsr=(direct)|utmccn=(direct)|utmcmd=(none); PHPSESSID=147ef1dc89f47d51871c9a7889879e8b; cmsa=1; smcx_87002_last_shown_at=1460451638907
HTTP_CONNECTION: keep-alive
HTTP_ACCEPT: text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8
HTTP_HOST: loco2energy.local
REDIRECT_STATUS: 200
REDIRECT_HANDLER: php-fastcgi
FCGI_ROLE: RESPONDER
PHP_SELF: /admin/core/settings/diagnostics/index.php
REQUEST_TIME_FLOAT: 1460455780.94
REQUEST_TIME: 1460455780
argc: 1