diff --git a/src/NzbDrone.Core.Test/TvTests/EpisodeServiceTests/HandleEpisodeFileDeletedFixture.cs b/src/NzbDrone.Core.Test/TvTests/EpisodeServiceTests/HandleEpisodeFileDeletedFixture.cs
index 6f90c9716..fe8e521b3 100644
--- a/src/NzbDrone.Core.Test/TvTests/EpisodeServiceTests/HandleEpisodeFileDeletedFixture.cs
+++ b/src/NzbDrone.Core.Test/TvTests/EpisodeServiceTests/HandleEpisodeFileDeletedFixture.cs
@@ -1,9 +1,11 @@
-using System.Collections.Generic;
+using System.Collections.Generic;
 using System.Linq;
 using FizzWare.NBuilder;
 using Moq;
 using NUnit.Framework;
+using NzbDrone.Common.Extensions;
 using NzbDrone.Core.Configuration;
+using NzbDrone.Core.Datastore;
 using NzbDrone.Core.MediaFiles;
 using NzbDrone.Core.MediaFiles.Events;
 using NzbDrone.Core.Test.Framework;
@@ -14,14 +16,20 @@ namespace NzbDrone.Core.Test.TvTests.EpisodeServiceTests
     [TestFixture]
     public class HandleEpisodeFileDeletedFixture : CoreTest<EpisodeService>
     {
+        private Series _series;
         private EpisodeFile _episodeFile;
         private List<Episode> _episodes;
 
         [SetUp]
         public void Setup()
         {
+            _series = Builder<Series>
+                .CreateNew()
+                .Build();
+
             _episodeFile = Builder<EpisodeFile>
                 .CreateNew()
+                .With(e => e.SeriesId = _series.Id)
                 .Build();
         }
 
@@ -30,6 +38,7 @@ namespace NzbDrone.Core.Test.TvTests.EpisodeServiceTests
             _episodes = Builder<Episode>
                 .CreateListOfSize(1)
                 .All()
+                .With(e => e.SeriesId = _series.Id)
                 .With(e => e.Monitored = true)
                 .Build()
                 .ToList();
@@ -44,6 +53,7 @@ namespace NzbDrone.Core.Test.TvTests.EpisodeServiceTests
             _episodes = Builder<Episode>
                 .CreateListOfSize(2)
                 .All()
+                .With(e => e.SeriesId = _series.Id)
                 .With(e => e.Monitored = true)
                 .Build()
                 .ToList();
@@ -85,9 +95,31 @@ namespace NzbDrone.Core.Test.TvTests.EpisodeServiceTests
                   .Returns(true);
 
             Subject.Handle(new EpisodeFileDeletedEvent(_episodeFile, DeleteMediaFileReason.MissingFromDisk));
+            Subject.HandleAsync(new SeriesScannedEvent(_series, new List<string>()));
 
             Mocker.GetMock<IEpisodeRepository>()
-                .Verify(v => v.ClearFileId(It.IsAny<Episode>(), true), Times.Once());
+                .Verify(v => v.SetMonitored(It.IsAny<IEnumerable<int>>(), false), Times.Once());
+        }
+
+        [Test]
+        public void should_leave_monitored_if_autoUnmonitor_is_true_and_missing_episode_is_replaced()
+        {
+            GivenSingleEpisodeFile();
+
+            var newEpisodeFile = _episodeFile.JsonClone();
+            newEpisodeFile.Id = 123;
+            newEpisodeFile.Episodes = new LazyLoaded<List<Episode>>(_episodes);
+
+            Mocker.GetMock<IConfigService>()
+                .SetupGet(s => s.AutoUnmonitorPreviouslyDownloadedEpisodes)
+                .Returns(true);
+
+            Subject.Handle(new EpisodeFileDeletedEvent(_episodeFile, DeleteMediaFileReason.MissingFromDisk));
+            Subject.Handle(new EpisodeFileAddedEvent(newEpisodeFile));
+            Subject.HandleAsync(new SeriesScannedEvent(_series, new List<string>()));
+
+            Mocker.GetMock<IEpisodeRepository>()
+                .Verify(v => v.SetMonitored(It.IsAny<IEnumerable<int>>(), false), Times.Never());
         }
 
         [Test]
diff --git a/src/NzbDrone.Core/Tv/EpisodeService.cs b/src/NzbDrone.Core/Tv/EpisodeService.cs
index 241037799..20dad0582 100644
--- a/src/NzbDrone.Core/Tv/EpisodeService.cs
+++ b/src/NzbDrone.Core/Tv/EpisodeService.cs
@@ -2,6 +2,7 @@ using System;
 using System.Collections.Generic;
 using System.Linq;
 using NLog;
+using NzbDrone.Common.Cache;
 using NzbDrone.Core.Configuration;
 using NzbDrone.Core.Datastore;
 using NzbDrone.Core.MediaFiles;
@@ -42,16 +43,19 @@ namespace NzbDrone.Core.Tv
     public class EpisodeService : IEpisodeService,
                                   IHandle<EpisodeFileDeletedEvent>,
                                   IHandle<EpisodeFileAddedEvent>,
-                                  IHandleAsync<SeriesDeletedEvent>
+                                  IHandleAsync<SeriesDeletedEvent>,
+                                  IHandleAsync<SeriesScannedEvent>
     {
         private readonly IEpisodeRepository _episodeRepository;
         private readonly IConfigService _configService;
+        private readonly ICached<HashSet<int>> _cache;
         private readonly Logger _logger;
 
-        public EpisodeService(IEpisodeRepository episodeRepository, IConfigService configService, Logger logger)
+        public EpisodeService(IEpisodeRepository episodeRepository, IConfigService configService, ICacheManager cacheManager, Logger logger)
         {
             _episodeRepository = episodeRepository;
             _configService = configService;
+            _cache = cacheManager.GetCache<HashSet<int>>(GetType());
             _logger = logger;
         }
 
@@ -215,34 +219,6 @@ namespace NzbDrone.Core.Tv
             _episodeRepository.DeleteMany(episodes);
         }
 
-        public void HandleAsync(SeriesDeletedEvent message)
-        {
-            var episodes = _episodeRepository.GetEpisodesBySeriesIds(message.Series.Select(s => s.Id).ToList());
-            _episodeRepository.DeleteMany(episodes);
-        }
-
-        public void Handle(EpisodeFileDeletedEvent message)
-        {
-            foreach (var episode in GetEpisodesByFileId(message.EpisodeFile.Id))
-            {
-                _logger.Debug("Detaching episode {0} from file.", episode.Id);
-
-                var unmonitorForReason = message.Reason != DeleteMediaFileReason.Upgrade &&
-                                         message.Reason != DeleteMediaFileReason.ManualOverride;
-
-                _episodeRepository.ClearFileId(episode, unmonitorForReason && _configService.AutoUnmonitorPreviouslyDownloadedEpisodes);
-            }
-        }
-
-        public void Handle(EpisodeFileAddedEvent message)
-        {
-            foreach (var episode in message.EpisodeFile.Episodes.Value)
-            {
-                _episodeRepository.SetFileId(episode, message.EpisodeFile.Id);
-                _logger.Debug("Linking [{0}] > [{1}]", message.EpisodeFile.RelativePath, episode);
-            }
-        }
-
         private Episode FindOneByAirDate(int seriesId, string date, int? part)
         {
             var episodes = _episodeRepository.Find(seriesId, date);
@@ -277,5 +253,73 @@ namespace NzbDrone.Core.Tv
 
             throw new InvalidOperationException($"Multiple episodes with the same air date found. Date: {date}");
         }
+
+        public void Handle(EpisodeFileDeletedEvent message)
+        {
+            foreach (var episode in GetEpisodesByFileId(message.EpisodeFile.Id))
+            {
+                _logger.Debug("Detaching episode {0} from file.", episode.Id);
+
+                var unmonitorEpisodes = _configService.AutoUnmonitorPreviouslyDownloadedEpisodes;
+
+                var unmonitorForReason = message.Reason != DeleteMediaFileReason.Upgrade &&
+                                         message.Reason != DeleteMediaFileReason.ManualOverride &&
+                                         message.Reason != DeleteMediaFileReason.MissingFromDisk;
+
+                // If episode is being unlinked because it's missing from disk store it for
+                if (message.Reason == DeleteMediaFileReason.MissingFromDisk && unmonitorEpisodes)
+                {
+                    lock (_cache)
+                    {
+                        var ids = _cache.Get(episode.SeriesId.ToString(), () => new HashSet<int>());
+
+                        ids.Add(episode.Id);
+                    }
+                }
+
+                _episodeRepository.ClearFileId(episode, unmonitorForReason && unmonitorEpisodes);
+            }
+        }
+
+        public void Handle(EpisodeFileAddedEvent message)
+        {
+            foreach (var episode in message.EpisodeFile.Episodes.Value)
+            {
+                _episodeRepository.SetFileId(episode, message.EpisodeFile.Id);
+
+                lock (_cache)
+                {
+                    var ids = _cache.Find(episode.SeriesId.ToString());
+
+                    if (ids?.Contains(episode.Id) == true)
+                    {
+                        ids.Remove(episode.Id);
+                    }
+                }
+
+                _logger.Debug("Linking [{0}] > [{1}]", message.EpisodeFile.RelativePath, episode);
+            }
+        }
+
+        public void HandleAsync(SeriesDeletedEvent message)
+        {
+            var episodes = _episodeRepository.GetEpisodesBySeriesIds(message.Series.Select(s => s.Id).ToList());
+            _episodeRepository.DeleteMany(episodes);
+        }
+
+        public void HandleAsync(SeriesScannedEvent message)
+        {
+            lock (_cache)
+            {
+                var ids = _cache.Find(message.Series.Id.ToString());
+
+                if (ids?.Any() == true)
+                {
+                    _episodeRepository.SetMonitored(ids, false);
+                }
+
+                _cache.Remove(message.Series.Id.ToString());
+            }
+        }
     }
 }