首先先給出解決方案
將EF版本6.2降級為6.13

Schema specified is not valid. Errors: The relationship ‘Service.Sys_Permission_Roles’ was not loaded because the type ‘Service.Sys_Permission’ is not available.
說明: 執行當前 Web 請求期間，出現未經處理的異常。請檢查堆疊跟蹤資訊，以瞭解有關該錯誤以及程式碼中導致錯誤的出處的詳細資訊。

異常詳細資訊: System.Data.Entity.Core.MetadataException: Schema specified is not valid. Errors: The relationship ‘Service.Sys_Permission_Roles’ was not loaded because the type ‘Service.Sys_Permission’ is not available.

堆疊跟蹤:

[MetadataException: Schema specified is not valid. Errors: The relationship ‘Service.Sys_Permission_Roles’ was not loaded because the type ‘Service.Sys_Permission’ is not available.]
System.Data.Entity.Core.Metadata.Edm.CodeFirstOSpaceTypeFactory.LogError(String errorMessage, EdmType relatedType) +44
System.Data.Entity.Core.Metadata.Edm.OSpaceTypeFactory.CreateAndAddNavigationProperty(StructuralType cspaceType, StructuralType ospaceType, NavigationProperty cspaceProperty) +820
System.Data.Entity.Core.Metadata.Edm.<>c__DisplayClass1a.b__16() +25
System.Data.Entity.Core.Metadata.Edm.CodeFirstOSpaceLoader.LoadTypes(EdmItemCollection edmItemCollection, ObjectItemCollection objectItemCollection) +393
System.Data.Entity.ModelConfiguration.Edm.DbDatabaseMappingExtensions.ToMetadataWorkspace(DbDatabaseMapping databaseMapping) +307
System.Data.Entity.Internal.CodeFirstCachedMetadataWorkspace.Create(DbDatabaseMapping databaseMapping) +23
System.Data.Entity.Infrastructure.DbModel.Compile() +15
System.Data.Entity.Internal.LazyInternalContext.CreateModel(LazyInternalContext internalContext) +211
System.Data.Entity.Internal.RetryLazy2.GetValue(TInput input) +123 System.Data.Entity.Internal.LazyInternalContext.InitializeContext() +616 System.Data.Entity.Internal.InternalContext.Initialize() +21 System.Data.Entity.Internal.InternalContext.GetEntitySetAndBaseTypeForType(Type entityType) +15 System.Data.Entity.Internal.Linq.InternalSet

1.Initialize() +53
System.Data.Entity.Internal.Linq.InternalSet1.get_InternalContext() +16 System.Data.Entity.Infrastructure.DbQuery1.System.Linq.IQueryable.get_Provider() +39
System.Linq.Queryable.Where(IQueryable1 source, Expression1 predicate) +83
Service.Sys_User_Service.CookieCheck(String cookieValue) in E:\DotNet\DotNet_WorkSpace\銀龍軟體官網\YL.Website.SoftManage\YL.WebAPP.SoftManage.Service\Sys_User_Service.cs:129
SoftManage.App_Start.CheckLoginAuthorizeFilter.OnAuthorization(AuthorizationContext filterContext) in E:\DotNet\DotNet_WorkSpace\銀龍軟體官網\YL.Website.SoftManage\YL.WebAPP.SoftManage\App_Start\Filter\CheckLoginAuthorizeFilter.cs:34
System.Web.Mvc.ControllerActionInvoker.InvokeAuthorizationFilters(ControllerContext controllerContext, IList1 filters, ActionDescriptor actionDescriptor) +97 System.Web.Mvc.Async.<>c__DisplayClass3_1.<BeginInvokeAction>b__0(AsyncCallback asyncCallback, Object asyncState) +640 System.Web.Mvc.Async.WrappedAsyncResult1.CallBeginDelegate(AsyncCallback callback, Object callbackState) +14
System.Web.Mvc.Async.WrappedAsyncResultBase1.Begin(AsyncCallback callback, Object state, Int32 timeout) +128 System.Web.Mvc.Async.AsyncControllerActionInvoker.BeginInvokeAction(ControllerContext controllerContext, String actionName, AsyncCallback callback, Object state) +346 System.Web.Mvc.<>c.<BeginExecuteCore>b__152_0(AsyncCallback asyncCallback, Object asyncState, ExecuteCoreState innerState) +27 System.Web.Mvc.Async.WrappedAsyncVoid1.CallBeginDelegate(AsyncCallback callback, Object callbackState) +30
System.Web.Mvc.Async.WrappedAsyncResultBase1.Begin(AsyncCallback callback, Object state, Int32 timeout) +128 System.Web.Mvc.Controller.BeginExecuteCore(AsyncCallback callback, Object state) +494 System.Web.Mvc.<>c.<BeginExecute>b__151_1(AsyncCallback asyncCallback, Object callbackState, Controller controller) +16 System.Web.Mvc.Async.WrappedAsyncVoid1.CallBeginDelegate(AsyncCallback callback, Object callbackState) +20
System.Web.Mvc.Async.WrappedAsyncResultBase1.Begin(AsyncCallback callback, Object state, Int32 timeout) +128 System.Web.Mvc.Controller.BeginExecute(RequestContext requestContext, AsyncCallback callback, Object state) +403 System.Web.Mvc.Controller.System.Web.Mvc.Async.IAsyncController.BeginExecute(RequestContext requestContext, AsyncCallback callback, Object state) +16 System.Web.Mvc.<>c.<BeginProcessRequest>b__20_0(AsyncCallback asyncCallback, Object asyncState, ProcessRequestState innerState) +54 System.Web.Mvc.Async.WrappedAsyncVoid1.CallBeginDelegate(AsyncCallback callback, Object callbackState) +30
System.Web.Mvc.Async.WrappedAsyncResultBase`1.Begin(AsyncCallback callback, Object state, Int32 timeout) +128
System.Web.Mvc.MvcHandler.BeginProcessRequest(HttpContextBase httpContext, AsyncCallback callback, Object state) +427
System.Web.Mvc.MvcHandler.BeginProcessRequest(HttpContext httpContext, AsyncCallback callback, Object state) +48
System.Web.Mvc.MvcHandler.System.Web.IHttpAsyncHandler.BeginProcessRequest(HttpContext context, AsyncCallback cb, Object extraData) +16
System.Web.CallHandlerExecutionStep.System.Web.HttpApplication.IExecutionStep.Execute() +103
System.Web.HttpApplication.ExecuteStepImpl(IExecutionStep step) +48
System.Web.HttpApplication.ExecuteStep(IExecutionStep step, Boolean& completedSynchronously) +159