Ok, looking through the scanner log again. I do not know why the episodes are not being put in the library.
Plex finds episodes 1,2 and 6, but that’s all. I do have some suggestions, which you will find at the end of my post.
Providing observation and log snippets.
Regarding missing episodes, Plex sees the files; however, it does not do anything with them.
Here, we see that Plex finds the media file (missing episode 1).
Jan 04, 2017 11:31:48.245 [0x7fcd3d2ed800] DEBUG - Adding file for scanner: /home/toby/media/TVShows/The Walking Dead/Season 7/The Walking Dead - s07e01 - The Day Will Come When You Won’t Be.mkv
That is the last mention of this item in the scanner log.
Comparing to an episode that shows up. Here we see that Plex finds the file.
Jan 04, 2017 11:31:48.244 [0x7fcd3d2ed800] DEBUG - Adding file for scanner: /home/toby/media/TVShows/The Walking Dead/Season 7/The Walking Dead - s07e04 - Service.mkv
And later in the log, Plex start the process of putting it into the library.
Jan 04, 2017 11:31:48.282 [0x7fcd3d2ed800] DEBUG - * Scanning The Walking Dead Season 7 Episode 4
Jan 04, 2017 11:31:48.282 [0x7fcd3d2ed800] DEBUG - Looking for path match for [/home/toby/media/TVShows/The Walking Dead/Season 7/The Walking Dead - s07e04 - Service.mkv]
Jan 04, 2017 11:31:48.283 [0x7fcd3d2ed800] DEBUG - Skipping hash check, no size match for 2530293723 bytes.
Jan 04, 2017 11:31:48.283 [0x7fcd3d2ed800] DEBUG - No match for hash.
Jan 04, 2017 11:31:48.283 [0x7fcd3d2ed800] DEBUG - Checking descendants of The Walking Dead
Jan 04, 2017 11:31:48.284 [0x7fcd3d2ed800] DEBUG - → Searching down into The Walking Dead/Season 7
Jan 04, 2017 11:31:48.284 [0x7fcd3d2ed800] DEBUG - Checking descendants of The Walking Dead/Season 7
Jan 04, 2017 11:31:48.285 [0x7fcd3d2ed800] DEBUG - → FOUND metadata item (show)
Jan 04, 2017 11:31:48.285 [0x7fcd3d2ed800] DEBUG - → We found a local media item with rooted metadata in The Walking Dead/Season 7
Jan 04, 2017 11:31:48.285 [0x7fcd3d2ed800] DEBUG - Found existing show 1126
Jan 04, 2017 11:31:48.286 [0x7fcd3d2ed800] DEBUG - Downloading document http://127.0.0.1:32400/library/changestamp
Jan 04, 2017 11:31:48.286 [0x7fcd3d2ed800] DEBUG - HTTP requesting GET http://127.0.0.1:32400/library/changestamp
Jan 04, 2017 11:31:48.287 [0x7fcd3d2ed800] DEBUG - HTTP 200 response from GET http://127.0.0.1:32400/library/changestamp
Jan 04, 2017 11:31:48.288 [0x7fcd3d2ed800] DEBUG - Added new metadata item () with ID 1129
Jan 04, 2017 11:31:48.288 [0x7fcd2e7ff700] DEBUG - HTTP requesting GET http://127.0.0.1:32400/:/metadata/flushMetadataCounterCache
Jan 04, 2017 11:31:48.289 [0x7fcd3d2ed800] DEBUG - Added new media item with ID=2824 (episode=4&episodic=1&season=7&show=The%20Walking%20Dead)
Jan 04, 2017 11:31:48.289 [0x7fcd2e7ff700] DEBUG - HTTP 200 response from GET http://127.0.0.1:32400/:/metadata/flushMetadataCounterCache
Jan 04, 2017 11:31:48.289 [0x7fcd3d2ed800] DEBUG - Added new media part with ID=2893 [/home/toby/media/TVShows/The Walking Dead/Season 7/The Walking Dead - s07e04 - Service.mkv]
If this was an issue of matching the episode, but not getting posters or metadata, I would suggest clearing the HTTP Cache for thetvdb, but that is not what is happening.
I do see that Plex is finding numerous other files inside the scanned location. Although, I wouldn’t think that would be an issue, maybe that is confusing the scanner. I also noticed in the plex media info xml for the episode you provided, that there is extra info that Plex is seeing - maybe that is causing issues.
Even though Plex isn’t supposed to use embedded metadata on MKV files, we have seen strange issues with title data on mkv files before where the file had been downloaded and the originator had sprayed their mark of sorts on the file.
From the Plex Media info xml (just a snippet).
<Stream id="6132" streamType="1" default="1" codec="h264" index="0" bitrate="5255" language="English" languageCode="eng" bitDepth="8" chromaSubsampling="4:2:0" colorRange="tv" colorSpace="bt709" frameRate="23.976" hasScalingMatrix="0" height="1076" level="40" profile="high" refFrames="4" requiredBandwidths="7371,6738,5979,5953,5953,5953,5953,5953" scanType="progressive" title="The.Walking.Dead.S07E05.1080p.WEB-DL.DD5.1.H264-RARBG" width="1916"/>
What I would do at this point.
Move the entire series outside of Plex.
Update the library, empty trash, clean bundles
Sanitize things:
Remove all the files which are not needed by Plex -.nfo, .xml, .jpg, .metathumb.
Disable Local media assets - Settings> Server> Agents> Shows> TheTVDB
Run the files through MKVToolNix and remove the unecessary tracks, track names and/or tags.
Move series back into scanned location, cross fingers, and update the library.