PMS logs show the following METADATA items were deleted as part of scanner activity.
[chuck@lizum user.2025]$ grep DELE *
Plex Media Server.1.log:Feb 22, 2025 13:24:56.205 [140652952967992] INFO - Request: [192.168.1.199:58020 (Allowed Network (Subnet))] DELETE /library/metadata/500131 (13 live) #628974 TLS GZIP Signed-in Token (spikemixture) (fs max)
Plex Media Server.1.log:Feb 22, 2025 13:24:56.918 [140653399325496] INFO - Completed: [192.168.1.199:58020] 200 DELETE /library/metadata/500131 (13 live) #628974 TLS GZIP 713ms 195 bytes (pipelined: 11)
Plex Media Server.1.log:Feb 22, 2025 13:29:39.112 [140652814760760] INFO - Request: [192.168.1.199:58626 (Allowed Network (Subnet))] DELETE /library/metadata/496273 (13 live) #628e5b TLS GZIP Signed-in Token (spikemixture) (fs max)
Plex Media Server.1.log:Feb 22, 2025 13:29:40.329 [140653397216056] INFO - Completed: [192.168.1.199:58626] 200 DELETE /library/metadata/496273 (13 live) #628e5b TLS GZIP 1217ms 195 bytes (pipelined: 3)
Plex Media Server.1.log:Feb 22, 2025 13:31:01.291 [140652746566456] INFO - Request: [192.168.1.199:58692 (Allowed Network (Subnet))] DELETE /library/metadata/496279 (18 live) #630412 TLS GZIP Signed-in Token (spikemixture) (fs max)
Plex Media Server.1.log:Feb 22, 2025 13:31:02.409 [140653397216056] INFO - Completed: [192.168.1.199:58692] 200 DELETE /library/metadata/496279 (15 live) #630412 TLS GZIP 1118ms 195 bytes (pipelined: 16)
Plex Media Server.1.log:Feb 22, 2025 13:32:34.598 [140652771879736] INFO - Request: [192.168.1.199:58776 (Allowed Network (Subnet))] DELETE /library/metadata/495449 (15 live) #631152 TLS GZIP Signed-in Token (spikemixture) (fs max)
Plex Media Server.1.log:Feb 22, 2025 13:32:35.349 [140653397216056] INFO - Completed: [192.168.1.199:58776] 200 DELETE /library/metadata/495449 (15 live) #631152 TLS GZIP 750ms 195 bytes (pipelined: 5)
Plex Media Server.1.log:Feb 22, 2025 13:34:25.453 [140652769770296] INFO - Request: [192.168.1.199:58794 (Allowed Network (Subnet))] DELETE /library/metadata/495448 (14 live) #631a50 TLS GZIP Signed-in Token (spikemixture) (fs max)
Plex Media Server.1.log:Feb 22, 2025 13:34:25.807 [140653399325496] INFO - Completed: [192.168.1.199:58794] 200 DELETE /library/metadata/495448 (14 live) #631a50 TLS GZIP 354ms 195 bytes (pipelined: 48)
Plex Media Server.1.log:Feb 22, 2025 13:34:49.984 [140652769770296] INFO - Request: [192.168.1.199:58810 (Allowed Network (Subnet))] DELETE /library/metadata/500130 (21 live) #631c32 TLS GZIP Signed-in Token (spikemixture) (fs max)
Plex Media Server.1.log:Feb 22, 2025 13:34:51.507 [140653399325496] INFO - Completed: [192.168.1.199:58810] 200 DELETE /library/metadata/500130 (19 live) #631c32 TLS GZIP 1522ms 195 bytes (pipelined: 6)
Plex Media Server.1.log:Feb 22, 2025 13:35:24.414 [140652765551416] INFO - Request: [192.168.1.199:58820 (Allowed Network (Subnet))] DELETE /library/metadata/495447 (19 live) #631e0c TLS GZIP Signed-in Token (spikemixture) (fs max)
Plex Media Server.1.log:Feb 22, 2025 13:35:24.975 [140653397216056] INFO - Completed: [192.168.1.199:58820] 200 DELETE /library/metadata/495447 (19 live) #631e0c TLS GZIP 561ms 195 bytes (pipelined: 6)
Plex Media Server.log:Feb 22, 2025 13:37:40.342 [140653049330488] INFO - Request: [192.168.1.199:58838 (Allowed Network (Subnet))] DELETE /library/metadata/495445 (11 live) #64f6b8 TLS GZIP Signed-in Token (spikemixture) (fs max)
Plex Media Server.log:Feb 22, 2025 13:37:40.768 [140653399325496] INFO - Completed: [192.168.1.199:58838] 200 DELETE /library/metadata/495445 (11 live) #64f6b8 TLS GZIP 425ms 195 bytes (pipelined: 15)
Plex Media Server.log:Feb 22, 2025 13:40:09.380 [140652806409016] INFO - Request: [192.168.1.199:58850 (Allowed Network (Subnet))] DELETE /library/metadata/495442 (22 live) #663ea9 TLS GZIP Signed-in Token (spikemixture) (fs max)
Plex Media Server.log:Feb 22, 2025 13:40:10.444 [140653397216056] INFO - Completed: [192.168.1.199:58850] 200 DELETE /library/metadata/495442 (22 live) #663ea9 TLS GZIP 1063ms 195 bytes (pipelined: 25)
[chuck@lizum user.2026]$
Of the metadata items removed, This media item was deleted (the file was no longer present)
Feb 22, 2025 13:37:40.750 [140653357038392] DEBUG - Skipping over directory 'Joe Cocker/THE VERY BEST OF', as nothing has changed; removing 1 media items from map.
Feb 22, 2025 13:37:40.750 [140653357038392] DEBUG - Activity: updated activity ed350c64-c84c-4da7-a90e-6273bc2db300 - completed 74.8% - Scanning music
Feb 22, 2025 13:37:40.751 [140653357038392] DEBUG - Scanner: Processing directory /share/CACHEDEV2_DATA/MEDIA/music/Joe Cocker/Legend Essential Collection (parent: yes)
Feb 22, 2025 13:37:40.762 [140653049330488] DEBUG - [Req#64f6b8] Deleting media item 1243961.
Feb 22, 2025 13:37:40.762 [140653049330488] DEBUG - [Req#64f6b8] Was connected to metadata item 495445, count is now 0.
Feb 22, 2025 13:37:40.763 [140653049330488] DEBUG - [Req#64f6b8] Destroying metadata item 495445 (OhMyHoles 25 01 13 Roxy Muray XXX 480p)
Feb 22, 2025 13:37:40.765 [140652824578872] DEBUG - [Req#64f6b8] [LibraryTimeline] Scanner activity on section 11: 0 added, 1 deleted
Feb 22, 2025 13:37:40.768 [140653399325496] INFO - Completed: [192.168.1.199:58838] 200 DELETE /library/metadata/495445 (11 live) #64f6b8 TLS GZIP 425ms 195 bytes (pipelined: 15)
Feb 22, 2025 13:37:40.808 [140653357038392] DEBUG - Skipping over directory 'Joe Cocker/Legend Essential Collection', as nothing has changed; removing 1 media items from map.
Do you have the Library option set to allow media deletion?
Could someone have hit delete from the browser
You’re 100% certain the files are physically gone ? (as viewed in FileStation)
EDIT: Do you have automation tools which could be deleting?