There is something going on with your media itself.
Here is an excerpt from your log. notice in PMS itself that the media is being ‘destroyed’ (when it thinks the media is gone / no longer where it used to be) only to be added again directly below.
what changes did you make? Is the media on a removable USB drive?
Oct 04, 2016 17:10:07.163 [0xe9335b40] DEBUG - Updating deletion state for metadata item 3619, is has a dead item count of 0.
Oct 04, 2016 17:10:07.165 [0xe9335b40] DEBUG - Deleting media item 7184.
Oct 04, 2016 17:10:07.167 [0xe9335b40] DEBUG - Was connected to metadata item 3619, count is now 0.
Oct 04, 2016 17:10:07.168 [0xe9335b40] DEBUG - Destroying metadata item 3619 (Going Bananas (Featurette))
Oct 04, 2016 17:10:07.172 [0xe9335b40] DEBUG - Deleting media item 7185.
Oct 04, 2016 17:10:07.174 [0xe9335b40] DEBUG - Was connected to metadata item 3620, count is now 2.
Oct 04, 2016 17:10:07.177 [0xe9335b40] DEBUG - Updating deletion state for metadata item 3620, is has a dead item count of 0.
Oct 04, 2016 17:10:07.179 [0xe9335b40] DEBUG - Deleting media item 7186.
Oct 04, 2016 17:10:07.182 [0xe9335b40] DEBUG - Was connected to metadata item 3620, count is now 1.
Oct 04, 2016 17:10:07.184 [0xe9335b40] DEBUG - Updating deletion state for metadata item 3620, is has a dead item count of 0.
Oct 04, 2016 17:10:07.186 [0xe9335b40] DEBUG - Deleting media item 7187.
Oct 04, 2016 17:10:07.188 [0xe9335b40] DEBUG - Was connected to metadata item 3620, count is now 0.
Oct 04, 2016 17:10:07.189 [0xe9335b40] DEBUG - Destroying metadata item 3620 (Mad Again (Featurette))
Oct 04, 2016 17:10:07.193 [0xe9335b40] DEBUG - Deleting media item 7188.
Oct 04, 2016 17:10:07.194 [0xe9335b40] DEBUG - Was connected to metadata item 3621, count is now 2.
Oct 04, 2016 17:10:07.196 [0xe9335b40] DEBUG - Updating deletion state for metadata item 3621, is has a dead item count of 0.
Oct 04, 2016 17:10:07.199 [0xe9335b40] DEBUG - Deleting media item 7189.
Oct 04, 2016 17:10:07.201 [0xe9335b40] DEBUG - Was connected to metadata item 3621, count is now 1.
Oct 04, 2016 17:10:07.202 [0xe9335b40] DEBUG - Updating deletion state for metadata item 3621, is has a dead item count of 0.
Oct 04, 2016 17:10:07.205 [0xe9335b40] DEBUG - Deleting media item 7190.
Oct 04, 2016 17:10:07.206 [0xe9335b40] DEBUG - Was connected to metadata item 3621, count is now 0.
Oct 04, 2016 17:10:07.208 [0xe9335b40] DEBUG - Destroying metadata item 3621 (On The Run (Featurette))
Oct 04, 2016 17:10:07.214 [0xe9335b40] DEBUG - Added new metadata item (Flash Gordon) with ID 3624
Oct 04, 2016 17:10:07.216 [0xe9335b40] DEBUG - Added new media item with ID=7193 ()
Oct 04, 2016 17:10:07.216 [0xe9335b40] DEBUG - Added new media part with ID=7203 []
Oct 04, 2016 17:10:07.217 [0xe9335b40] DEBUG - Updating part with ID=7203 []
Oct 04, 2016 17:10:07.218 [0xe9335b40] DEBUG - Added new media item with ID=7194 ()
Oct 04, 2016 17:10:07.219 [0xe9335b40] DEBUG - Added new media part with ID=7204 []
Oct 04, 2016 17:10:07.219 [0xe9335b40] DEBUG - Updating part with ID=7204 []
Oct 04, 2016 17:10:07.220 [0xe9335b40] DEBUG - Added new media item with ID=7195 ()
Oct 04, 2016 17:10:07.221 [0xe9335b40] DEBUG - Added new media part with ID=7205 []
Oct 04, 2016 17:10:07.221 [0xe9335b40] DEBUG - Updating part with ID=7205 []
Oct 04, 2016 17:10:07.222 [0xe9335b40] WARN - Held transaction for too long (../Library/MetadataItem.cpp:5822): 0.110000 seconds
Oct 04, 2016 17:10:07.309 [0xe9335b40] DEBUG - Loading information from media bundle for part ID 7185 from /volume1/Plex/Library/Application Support/Plex Media Server/Media/localhost/4/83fa16039d7835ce86162817ea8b6e13c5b9993e6.bundle/Contents
Oct 04, 2016 17:10:07.310 [0xe9335b40] DEBUG - Loaded metadata for Flash Gordon (ID 3616) in 210.000000 ms
Oct 04, 2016 17:10:07.310 [0xe9335b40] DEBUG - There was a change for metadata item 3616 (Flash Gordon), saving.
Oct 04, 2016 17:10:07.310 [0xe9335b40] DEBUG - Updating metadata item (save) (Flash Gordon) with ID 3616