It happened yesterday, I thought it might be a database issues, so I started over with and empty database, but today it did it again.
Version 2.0.0.3357
Mono Version 4.0.4 (Stable 4.0.4.1/5ab4c0d Mon Sep 14 09:24:50 UTC 2015)
I started seeing lots of these messages in the log, and eventually my library is empty.
NzbDrone.Core.Datastore.ModelNotFoundException: Series with ID 45 does not exist
at NzbDrone.Core.Datastore.BasicRepository`1[NzbDrone.Core.Tv.Series].Get (Int32 id) [0x00000] in :0
at NzbDrone.Core.Tv.SeriesService.GetSeries (Int32 seriesId) [0x00000] in :0
at NzbDrone.Core.IndexerSearch.NzbSearchService.SeasonSearch (Int32 seriesId, Int32 seasonNumber, Boolean missingOnly) [0x00000] in :0
at NzbDrone.Core.IndexerSearch.SeriesSearchService.Execute (NzbDrone.Core.IndexerSearch.SeriesSearchCommand message) [0x00000] in :0
at NzbDrone.Core.Messaging.Commands.CommandExecutor.ExecuteCommand[SeriesSearchCommand] (NzbDrone.Core.IndexerSearch.SeriesSearchCommand command, NzbDrone.Core.Messaging.Commands.CommandMode
l commandModel) [0x00000] in :0