MakeMKV maps all the episodes together in the Segment map. All the episodes are seperate files on the actual blu-ray disc.
I have backed up the 3 discs from Season 2 and removed the *.m2ts files and uploaded it here:
https://drive.google.com/open?id=0BypG0 ... k1fV19WQ0k
Season 3:
https://drive.google.com/open?id=0BypG0 ... DlscjJSVXM
Season 2
Disc 1
Disc Information
Label: STAR_WARS_CLONE_WARS_S2_BOX
Timestamp: 2010-08-21 01:09:58
Data capacity: 28.75 Gb
Disc type: BD-ROM
Number of layers: 2
Channel bit length: 74,5 nm (25.0 GB max. per layer)
Bus encryption flags: 80
Title information
Name: STAR WARS: THE CLONE WARS SEASON 2 (English)
Source file name: 00100.mpls
Duration: 3:00:38
Chapters count: 32
Size: 23.1 GB
Segment count: 8
Segment map: 163,166,167,168,169,170,171,172
File name: STAR_WARS_THE_CLONE_WARS_SEASON_2_t00.mkv
Disc 2
Disc Information
Label: STAR_WARS_CLONE_WARS_S2_BOX
Timestamp: 2010-08-21 02:42:27
Data capacity: 24.99 Gb
Disc type: BD-ROM
Number of layers: 2
Channel bit length: 74,5 nm (25.0 GB max. per layer)
Title information
Name: STAR WARS: THE CLONE WARS SEASON 2 (English)
Source file name: 00100.mpls
Duration: 2:37:22
Chapters count: 28
Size: 21.4 GB
Segment count: 7
Segment map: 76,135,136,137,143,144,145
File name: STAR_WARS_THE_CLONE_WARS_SEASON_2_t00.mkv
Season 3Disc 3
Disc Information
Label: STAR_WARS_CLONE_WARS_S2_BOX
Timestamp: 2010-08-19 17:48:33
Data capacity: 25.1 Gb
Disc type: BD-ROM
Number of layers: 2
Channel bit length: 74,5 nm (25.0 GB max. per layer)
Bus encryption flags: 80
Title information
Name: STAR WARS: THE CLONE WARS SEASON 2 (English)
Source file name: 00100.mpls
Duration: 2:37:43
Chapters count: 28
Size: 20.7 GB
Segment count: 7
Segment map: 144,145,146,147,148,149,150
File name: STAR_WARS_THE_CLONE_WARS_SEASON_2_t00.mkv
Disc 1
Disc Information
Label: SWCWBD02_S3D1
Timestamp: 2011-10-19 15:30:54
Data capacity: 24.96 Gb
Disc type: BD-ROM
Number of layers: 2
Channel bit length: 74,5 nm (25.0 GB max. per layer)
Title information
Name: STAR WARS: THE CLONE WARS SEASON 3 (English)
Source file name: 00100.mpls
Duration: 2:35:56
Chapters count: 28
Size: 21.6 GB
Segment count: 7
Segment map: 71,72,73,74,75,76,77
File name: STAR_WARS_THE_CLONE_WARS_SEASON_3_t00.mkv
Disc 2
Disc Information
Label: SWCW_S3D2
Timestamp: 2011-10-19 17:08:18
Data capacity: 27.39 Gb
Disc type: BD-ROM
Number of layers: 2
Channel bit length: 74,5 nm (25.0 GB max. per layer)
Title information
Name: STAR WARS: THE CLONE WARS SEASON 3 (English)
Source file name: 00100.mpls
Duration: 2:35:57
Chapters count: 28
Size: 21.4 GB
Segment count: 7
Segment map: 71,72,73,74,75,76,77
File name: STAR_WARS_THE_CLONE_WARS_SEASON_3_t00.mkv
Disc 3
Disc Information
Label: SWCW_S3D3
Timestamp: 2011-10-20 15:46:30
Data capacity: 29.79 Gb
Disc type: BD-ROM
Number of layers: 2
Channel bit length: 74,5 nm (25.0 GB max. per layer)
Title information
Name: STAR WARS: THE CLONE WARS SEASON 3 (English)
Source file name: 00100.mpls
Duration: 2:59:10
Chapters count: 32
Size: 25.2 GB
Segment count: 8
Segment map: 71,72,73,74,75,76,77,81
File name: STAR_WARS_THE_CLONE_WARS_SEASON_3_t00.mkv