After upgrading certain shows need manual metadata refresh after every scan

Is R:\ a network drive? If so, check your network connection. There are several hundred network error messages in the log files for multiple shows. Entries from your log files are below.

Also, clean up the naming.

Neither of these align very well with Plex naming requirements:
R:\TV\King of the Hill\King.of.the.Hill.S13.1080p.WEB-DL.DD5.1.H.264-NTb\King.of.the.Hill.S13E01.Dia-BILL-ic.Shock.1080p.WEB-DL.DD5.1.H.264-NTb.mkv

R:\TV\King of the Hill\King.Of.The.Hill.S13E20.1080p.BluRay.x264-DEiMOS.mkv

At a minimum, add a season folder. Adding the year helps as well.
After renaming and reorganizing, Plex Dance the entire show.

R:\TV\King of the Hill (1997)\Season 13\King of the Hill (1997) s13e20 [1080p.etc].mkv

Naming and Organizing Your TV Show Files


Feb 07, 2022 19:00:56.185 [112944] WARN - Error scanning directory, we'll skip and continue: boost::filesystem::directory_iterator::construct: An unexpected network error occurred: "R:\TV\King of the Hill\King.Of.The.Hill.s08.WEB-DL.AAC.2.0.H264-BTN"
Feb 07, 2022 19:00:56.185 [112944] DEBUG - Scanner: Processing directory R:\TV\King of the Hill\King.of.the.Hill.S07.WEB-DL.AAC.2.0.H.264-BTN (parent: yes)
Feb 07, 2022 19:00:56.185 [104656] DEBUG - Path matched, we're reusing media item 1285337
Feb 07, 2022 19:00:56.186 [104656] DEBUG - Bringing back media item 1285337 to life.
Feb 07, 2022 19:00:56.186 [112944] WARN - Error scanning directory, we'll skip and continue: boost::filesystem::directory_iterator::construct: An unexpected network error occurred: "R:\TV\King of the Hill\King.of.the.Hill.S07.WEB-DL.AAC.2.0.H.264-BTN"
Feb 07, 2022 19:00:56.186 [112944] DEBUG - Scanner: Processing directory R:\TV\King of the Hill\King.of.the.Hill.S06.480p.WEB-DL.AAC2.0.H.264-SA89 (parent: yes)
Feb 07, 2022 19:00:56.186 [104656] DEBUG - Updating deletion state for metadata item 155177, is has a dead item count of 1.
Feb 07, 2022 19:00:56.186 [104656] DEBUG - Updating deletion state for metadata item 155174, is has a dead item count of 24.
Feb 07, 2022 19:00:56.187 [104656] DEBUG - Updating deletion state for metadata item 155173, is has a dead item count of 13.
Feb 07, 2022 19:00:56.187 [112944] WARN - Error scanning directory, we'll skip and continue: boost::filesystem::directory_iterator::construct: An unexpected network error occurred: "R:\TV\King of the Hill\King.of.the.Hill.S06.480p.WEB-DL.AAC2.0.H.264-SA89"
Feb 07, 2022 19:00:56.187 [112944] DEBUG - Scanner: Processing directory R:\TV\King of the Hill\King.of.the.Hill.S05.480p.WEB-DL.AAC2.0.H.264-SA89 (parent: yes)
Feb 07, 2022 19:00:56.187 [104656] DEBUG - Looking for path match for [R:\TV\King of the Hill\King.Of.The.Hill.S13E23.1080p.BluRay.x264-DEiMOS.mkv]
Feb 07, 2022 19:00:56.188 [104656] DEBUG - Path matched, we're reusing media item 1285338
Feb 07, 2022 19:00:56.188 [104656] DEBUG - Bringing back media item 1285338 to life.
Feb 07, 2022 19:00:56.188 [112944] WARN - Error scanning directory, we'll skip and continue: boost::filesystem::directory_iterator::construct: An unexpected network error occurred: "R:\TV\King of the Hill\King.of.the.Hill.S05.480p.WEB-DL.AAC2.0.H.264-SA89"