Deleted recordings not being moved to Trash, "File xx didn't exist, can't skip" error

I am using a scanner based on Plex-EyeTV-Tools - my fork is here - GitHub - steco/Plex-EyeTV-Tools: Plex EyeTV Tools: Scanner and Agent (information) Bundle.

The scanner works perfectly, there’s just one problem with it. If I remove media from the directory manually (ie not from within Plex) it doesn’t reflect in Plex. The entries I see in the scanner log after I had manually removed “Britain’s Biggest Warship (2018) - S01E03 - Out With the Old In With the New.ts” are :

Aug 04, 2018 15:54:16.457 [0x7fffa5243380] DEBUG - * Scanning directory /Volumes/MyBook HD/EyeTV/EyeTV Archive/Britain’s Biggest Warship (2018) (parent: yes)
Aug 04, 2018 15:54:16.457 [0x7fffa5243380] DEBUG - Adding file for scanner: “/Volumes/MyBook HD/EyeTV/EyeTV Archive/Britain’s Biggest Warship (2018)/.DS_Store”
Aug 04, 2018 15:54:16.457 [0x7fffa5243380] DEBUG - Adding subdirectory for scanner: “/Volumes/MyBook HD/EyeTV/EyeTV Archive/Britain’s Biggest Warship (2018)/Season 01”
Aug 04, 2018 15:54:16.530 [0x7fffa5243380] DEBUG - Skipping over directory ‘Britain’s Biggest Warship (2018)’, as nothing has changed; removing 0 media items from map.
Aug 04, 2018 15:54:16.530 [0x7fffa5243380] DEBUG - * Scanning directory /Volumes/MyBook HD/EyeTV/EyeTV Archive/Britain’s Biggest Warship (2018)/Season 01 (parent: yes)
Aug 04, 2018 15:54:16.530 [0x700010269000] DEBUG - HTTP requesting GET http://127.0.0.1:32400/:/metadata/updateProgressMessage?message=Scanning%20Britain’s%20Biggest%20Warship%20(2018)\
Aug 04, 2018 15:54:16.531 [0x7fffa5243380] DEBUG - Adding file for scanner: “/Volumes/MyBook HD/EyeTV/EyeTV Archive/Britain’s Biggest Warship (2018)/Season 01/.DS_Store”
Aug 04, 2018 15:54:16.531 [0x7fffa5243380] DEBUG - Adding file for scanner: “/Volumes/MyBook HD/EyeTV/EyeTV Archive/Britain’s Biggest Warship (2018)/Season 01/Britain’s Biggest Warship (2018) - S01E02 - In at the Deep End (copy 1).ts”
Aug 04, 2018 15:54:16.532 [0x700010269000] DEBUG - HTTP 200 response from GET http://127.0.0.1:32400/:/metadata/updateProgressMessage?message=Scanning%20Britain’s%20Biggest%20Warship%20(2018)\
Aug 04, 2018 15:54:16.537 [0x7fffa5243380] DEBUG - File ‘/Volumes/MyBook HD/EyeTV/EyeTV Archive/Britain’s Biggest Warship (2018)/Season 01/Britain’s Biggest Warship (2018) - S01E03 - Out With the Old In With the New.ts’ didn’t exist, can’t skip.

Can someone explain what might be causing this, and if there is something I can change in the scanner to resolve it?

Thanks

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