missing media names still present

[Kristy21]

no, THEY are those files, only renamed.

for example, first file from the log:

Media not found at "/media/Series/Star Trek Voyager/Season 1/Behind The Scenes/01 Voyager.Time.Capsule.Kathryn.Janeway.DVDRip.x264-MARS.mkv" for item ddcf77c2-023c-d201-eff5-96685600eb8e

is now renamed into "S01 Voyager.Time.Capsule.Kathryn.Janewaynull’s brawlbehindthescenes.mkv"

...only if server handles behind the scenes folder as playlist?
IDK, possible?

Given the Synology Docker setup, where exactly are the Trickplay image files (.bif files) being stored, and have you checked if they are still present under the old item ID structure or if the files for those item IDs are simply missing?