So, where in those logs did you manually trigger your library update? Did you turn off your libraryautoupdate services?
17:11:33 2405.400146 T:1562887072 DEBUG: JSONRPC: Incoming request: {"jsonrpc":"2.0","method":"VideoLibrary.Scan","id":1} 17:11:33 2405.405273 T:1562887072 DEBUG: CWebServer[8080] [OUT] Accept-Ranges: none 17:11:33 2405.405273 T:1562887072 DEBUG: CWebServer[8080] [OUT] Cache-Control: private, max-age=0, no-cache 17:11:33 2405.405518 T:1562887072 DEBUG: CWebServer[8080] [OUT] Content-Length: 38 17:11:33 2405.405518 T:1562887072 DEBUG: CWebServer[8080] [OUT] Content-Type: application/json 17:11:33 2405.405518 T:1562887072 DEBUG: CWebServer[8080] [OUT] HTTP/1.1 200 /jsonrpc?VideoLibrary.Scan 17:11:33 2405.457275 T:1552937888 NOTICE: VideoInfoScanner: Starting scan .. 17:11:33 2405.457520 T:1962718112 DEBUG: CAnnouncementManager - Announcement: OnScanStarted from xbmc 17:11:33 2405.457764 T:1962718112 DEBUG: GOT ANNOUNCEMENT, type: 16, from xbmc, message OnScanStarted