
The
Import companion files feature is correctly moving
Scenes folder is moved along as best as I can tell. Here's what I get:
Console Output: Select all
INPUT
└── Movies
└── 300- Rise of an Empire
├── 300 Rise of an Empire_t01.mkv
└── Scenes
├── SceneA.mkv
└── SceneB.mkv
OUTPUT
└── Movies
└── 300 - Rise of an Empire (2014) {tmdb-53182}
├── 300 - Rise of an Empire (2014).mkv
└── Scenes
├── SceneA.mkv
└── SceneB.mkv

I get the same results in both GUI and CLI:
Console Output: Select all
$ filebot -rename -r "INPUT" --output "OUTPUT" --db TheMovieDB -non-strict --format "{plex.id}" --apply import
Rename movies using [TheMovieDB]
Auto-detect movie from context [INPUT/Movies/300- Rise of an Empire/300 Rise of an Empire_t01 copy.mkv]
[MOVE] from [INPUT/Movies/300- Rise of an Empire/300 Rise of an Empire_t01 copy.mkv] to [OUTPUT/Movies/300 - Rise of an Empire (2014) {tmdb-53182}/300 - Rise of an Empire (2014).mkv]
[IMPORT] Moving SceneA.mkv (OUTPUT/Movies/300 - Rise of an Empire (2014) {tmdb-53182}/Scenes/SceneA.mkv)
[IMPORT] Moving SceneB.mkv (OUTPUT/Movies/300 - Rise of an Empire (2014) {tmdb-53182}/Scenes/SceneB.mkv)

Can you spot any notable difference between what you're doing and what I'm doing that might cause different behaviour?

What custom format are you using?

What does
System Information say?