Fix: Go to Settings -> Misc to set your preference for automatically ignoring deleted episodes (false by default).

NzbDrone.Web/Controllers/SettingsController.cs

@@ -232,6 +232,7 @@ namespace NzbDrone.Web.Controllers
         {
             var model = new MiscSettingsModel();
             model.EnableBacklogSearching = _configProvider.EnableBacklogSearching;
+            model.AutoIgnorePreviouslyDownloadedEpisodes = _configProvider.AutoIgnorePreviouslyDownloadedEpisodes;
 
             return View(model);
         }
@@ -591,6 +592,7 @@ namespace NzbDrone.Web.Controllers
             if (ModelState.IsValid)
             {
                 _configProvider.EnableBacklogSearching = data.EnableBacklogSearching;
+                _configProvider.AutoIgnorePreviouslyDownloadedEpisodes = data.AutoIgnorePreviouslyDownloadedEpisodes;
 
                 return GetSuccessResult();
             }

NzbDrone.Web/Models/MiscSettingsModel.cs

@@ -11,5 +11,9 @@ namespace NzbDrone.Web.Models
         [DisplayName("Enable Backlog Searching")]
         [Description("Should NzbDrone try to download missing episodes automatically?")]
         public bool EnableBacklogSearching { get; set; }
+
+        [DisplayName("Automatically Ignore Deleted Episodes")]
+        [Description("Should NzbDrone automatically ignore episodes that were deleted from disk?")]
+        public bool AutoIgnorePreviouslyDownloadedEpisodes { get; set; }
     }
 }

NzbDrone.Web/Views/Settings/Misc.cshtml

@@ -9,6 +9,11 @@
         </label>
         @Html.CheckBoxFor(m => m.EnableBacklogSearching, new { @class = "inputClass checkClass" })
 
+        <label class="labelClass">@Html.LabelFor(m => m.AutoIgnorePreviouslyDownloadedEpisodes)
+            <span class="small">@Html.DescriptionFor(m => m.AutoIgnorePreviouslyDownloadedEpisodes)</span>
+        </label>
+        @Html.CheckBoxFor(m => m.AutoIgnorePreviouslyDownloadedEpisodes, new { @class = "inputClass checkClass" })
+
         <div style="overflow: hidden; height: 50px;">
         </div>