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 discs and removed the *.m2ts files and uploaded it here:
https://drive.google.com/open?id=0BypG0 ... XgxeHN6YW8
CHUCK_SEASON_2_DISC_1
Name: Chuck Season 2 Disc 1 (English)
Source file name: 00001.mpls
Duration: 4:19:54
Chapters count: 43
Size: 36.8 GB
Segment count: 6
Segment map: 6,16,7,18,8,20
File name: Chuck_Season_2_Disc_1_t00.mkv
CHUCK_SEASON_2_DISC_2
Name: Chuck Season 2 Disc 2 (English)
Source file name: 00001.mpls
Duration: 4:16:55
Chapters count: 44
Size: 37.2 GB
Segment count: 6
Segment map: 16,7,8,18,1,6
File name: Chuck_Season_2_Disc_2_t00.mkv
CHUCK_SEASON_2_DISC_3
Name: Chuck Season 2 Disc 3 (English)
Source file name: 00001.mpls
Duration: 4:18:07
Chapters count: 43
Size: 36.6 GB
Segment count: 6
Segment map: 14,6,16,7,18,1
File name: Chuck_Season_2_Disc_3_t00.mkv
CHUCK_SEASON_2_DISC_4
Name: Chuck Season 2 (English)
Source file name: 00001.mpls
Duration: 2:52:11
Chapters count: 32
Size: 24.0 GB
Segment count: 4
Segment map: 6,16,7,18
File name: Chuck_Season_2_t01.mkv