Files missing from backups

Our backup file storing programs perform a compare of the file size to a target file size. It raises a warning if a backup file is below target. We have had two warnings in the last week which has revealed that files are being dropped from the backup.

Comparing backups using WinMerge we found:

All except two recent backups are around 70,600KB (the site is a relatively static one). The two that are smaller are missing files:

1. 26/6 backup is missing files from folder /wp-content/uploads/2025/05
2. 30/6 backup is missing files from folder /wp-content/uploads/2023/01

This is the backup log for 26/6:

[INFO] BackWPup 5.7.2; A project of WP Media
[INFO] WordPress 6.9.4 on https://cyclehayling.org/
[INFO] Log Level: Normal (translated)
[INFO] BackWPup job: Files & Database
[INFO] Logfile is: backwpup_log_1af57b_2026-06-26_02-01-03.html
[INFO] Backup file is located at: /homepages/1/d937068188/htdocs/clickandbuilds/CycleHayling/.../2026-06-26_02-01-03_J3Y5BAOW01_FILE-DBDUMP-WPPLUGIN.zip
[2026-06-26 01:01:03 UTC] 1. Try to backup database …
[2026-06-26 01:01:03 UTC] Connected to database dbs8843343 on db5010438551.hosting-data.io
[2026-06-26 01:01:05 UTC] Added database dump "local.sql" with 11.92 MB to backup file list
[2026-06-26 01:01:05 UTC] Database backup done!
[2026-06-26 01:01:05 UTC] 1. Trying to make a list of folders to back up …
[2026-06-26 01:01:10 UTC] 406 folders to backup.
[2026-06-26 01:01:11 UTC] 1. Trying to generate a file with installed plugin names …
[2026-06-26 01:01:11 UTC] Added plugin list file "Cycle-Hayling.pluginlist.2026-06-26.txt" with 3.21 KB to backup file list.
[2026-06-26 01:01:11 UTC] 1. Trying to generate a manifest file …
[2026-06-26 01:01:11 UTC] Added manifest.json file with 5.32 KB to backup file list.
[2026-06-26 01:01:11 UTC] 1. Trying to create backup archive …
[2026-06-26 01:01:11 UTC] Compressing files as ZipArchive. Please be patient, this may take a moment.
[2026-06-26 01:02:08 UTC] After restrat on folder: wp-content/plugins/wp-update-mail-notification/vendor/symfony/polyfill-mbstring/
[2026-06-26 01:03:06 UTC] After restrat on folder: wp-content/uploads/2025/05/
[2026-06-26 01:03:08 UTC] Backup archive created.
[2026-06-26 01:03:08 UTC] Archive size is 62.99 MB.
[2026-06-26 01:03:08 UTC] 2535 Files with 89.60 MB in Archive.
[2026-06-26 01:03:08 UTC] 1 old log deleted
[2026-06-26 01:03:08 UTC] Job done in 125 seconds.

This is the backup log for 30/6:

[INFO] BackWPup 5.7.3; A project of WP Media
[INFO] WordPress 6.9.4 on https://cyclehayling.org/
[INFO] Log Level: Normal (translated)
[INFO] BackWPup job: Files & Database
[INFO] Logfile is: backwpup_log_21bf3d_2026-06-30_02-01-02.html
[INFO] Backup file is located at: /homepages/1/d937068188/htdocs/clickandbuilds/CycleHayling/.../2026-06-30_02-01-02_PHY5BAOR01_FILE-DBDUMP-WPPLUGIN.zip
[2026-06-30 01:01:02 UTC] 1. Try to backup database …
[2026-06-30 01:01:03 UTC] Connected to database dbs8843343 on db5010438551.hosting-data.io
[2026-06-30 01:01:04 UTC] Added database dump "local.sql" with 11.94 MB to backup file list
[2026-06-30 01:01:04 UTC] Database backup done!
[2026-06-30 01:01:04 UTC] 1. Trying to make a list of folders to back up …
[2026-06-30 01:01:08 UTC] 406 folders to backup.
[2026-06-30 01:01:09 UTC] 1. Trying to generate a file with installed plugin names …
[2026-06-30 01:01:09 UTC] Added plugin list file "Cycle-Hayling.pluginlist.2026-06-30.txt" with 3.21 KB to backup file list.
[2026-06-30 01:01:09 UTC] 1. Trying to generate a manifest file …
[2026-06-30 01:01:09 UTC] Added manifest.json file with 5.32 KB to backup file list.
[2026-06-30 01:01:09 UTC] 1. Trying to create backup archive …
[2026-06-30 01:01:09 UTC] Compressing files as ZipArchive. Please be patient, this may take a moment.
[2026-06-30 01:02:07 UTC] After restrat on folder: wp-content/plugins/tinymce-advanced/
[2026-06-30 01:03:04 UTC] After restrat on folder: wp-content/uploads/2023/01/
[2026-06-30 01:03:13 UTC] Backup archive created.
[2026-06-30 01:03:13 UTC] Archive size is 59.06 MB.
[2026-06-30 01:03:14 UTC] 2508 Files with 85.64 MB in Archive.
[2026-06-30 01:03:14 UTC] 1 old log deleted
[2026-06-30 01:03:14 UTC] Job done in 132 seconds.

Note that each problem folder was created at a restart (not restrat). Other backups are complete and a consistent size so this is not an access rights issue.

Looking across backups from other sites we also see unexpected drops in backup file sizes. This is obviously a serious concern.

Happy to provide further diagnostics.

Andy