Exchange 2013 issues after CU9 - updates

Question

I have a MS Exchange 2013 server that worked fine until I installed CU9 KB3087126.
Issues:
ECP is not accesible from the outside.
ECP is accessible from the inside using "https://server_name/ecp" but after entering the credentials I get a page with "Server Error in '/ecp' Application."
Could not load file or assembly 'Microsoft.Exchange.Common, Version=15.0.0.0, Culture=neutral, PublicKeyToken=token_here' or one of its dependencies. The system cannot find the file specified.
Description: An unhandled exception occurred during the execution of the current web request. Please review the stack trace for more information about the error and where it originated in the code.
Exception Details: System.IO.FileNotFoundException: Could not load file or assembly 'Microsoft.Exchange.Common, Version=15.0.0.0, Culture=neutral, PublicKeyToken=token_here' or one of its dependencies. The system cannot find the file specified.
Source Error:
An unhandled exception was generated during the execution of the current web request. Information regarding the origin and location of the exception can be identified using the exception stack trace below.
Assembly Load Trace: The following information can be helpful to determine why the assembly 'Microsoft.Exchange.Common, Version=15.0.0.0, Culture=neutral, PublicKeyToken=token_here' could not be loaded.
WRN: Assembly binding logging is turned OFF.
To enable assembly bind failure logging, set the registry value [HKLM\Software\Microsoft\Fusion!EnableLog] (DWORD) to 1.
Note: There is some performance penalty associated with assembly bind failure logging.
To turn this feature off, remove the registry value [HKLM\Software\Microsoft\Fusion!EnableLog].
Stack Trace:
[FileNotFoundException: Could not load file or assembly 'Microsoft.Exchange.Common, Version=15.0.0.0, Culture=neutral, PublicKeyToken=token_here' or one of its dependencies. The system cannot find the file specified.]
System.RuntimeTypeHandle.GetTypeByName(String name, Boolean throwOnError, Boolean ignoreCase, Boolean reflectionOnly, StackCrawlMarkHandle stackMark, IntPtr pPrivHostBinder, Boolean loadTypeFromPartialName, ObjectHandleOnStack type) +0
System.RuntimeTypeHandle.GetTypeByName(String name, Boolean throwOnError, Boolean ignoreCase, Boolean reflectionOnly, StackCrawlMark& stackMark, IntPtr pPrivHostBinder, Boolean loadTypeFromPartialName) +153
System.Type.GetType(String typeName, Boolean throwOnError, Boolean ignoreCase) +63
System.Web.Compilation.BuildManager.GetType(String typeName, Boolean throwOnError, Boolean ignoreCase) +124
System.Web.Configuration.ConfigUtil.GetType(String typeName, String propertyName, ConfigurationElement configElement, XmlNode node, Boolean checkAptcaBit, Boolean ignoreCase) +76
>[ConfigurationErrorsException: Could not load file or assembly 'Microsoft.Exchange.Common, Version=15.0.0.0, Culture=neutral, PublicKeyToken=token_here' or one of its dependencies. The system cannot find the file specified.]
System.Web.Configuration.ConfigUtil.GetType(String typeName, String propertyName, ConfigurationElement configElement, XmlNode node, Boolean checkAptcaBit, Boolean ignoreCase) [phone]
System.Web.Configuration.Common.ModulesEntry.SecureGetType(String typeName, String propertyName, ConfigurationElement configElement) +69
System.Web.Configuration.Common.ModulesEntry..ctor(String name, String typeName, String propertyName, ConfigurationElement configElement) +62
System.Web.HttpApplication.BuildIntegratedModuleCollection(List`1 moduleList) +299
System.Web.HttpApplication.GetModuleCollection(IntPtr appContext) +1262
System.Web.HttpApplication.RegisterEventSubscriptionsWithIIS(IntPtr appContext, HttpContext context, MethodInfo[] handlers) +133
System.Web.HttpApplication.InitSpecial(HttpApplicationState state, MethodInfo[] handlers, IntPtr appContext, HttpContext context) +304
System.Web.HttpApplicationFactory.GetSpecialApplicationInstance(IntPtr appContext, HttpContext context) +404
System.Web.Hosting.PipelineRuntime.InitializeApplication(IntPtr appContext) +475
[HttpException (0x80004005): Could not load file or assembly 'Microsoft.Exchange.Common, Version=15.0.0.0, Culture=neutral, PublicKeyToken=token_here' or one of its dependencies. The system cannot find the file specified.]
System.Web.HttpRuntime.FirstRequestInit(HttpContext context) [phone]
System.Web.HttpRuntime.EnsureFirstRequestInit(HttpContext context) +159
System.Web.HttpRuntime.ProcessRequestNotificationPrivate(IIS7WorkerRequest wr, HttpContext context) [phone]
In the Event log I have a WARNING from ASP.NET 4.0.30319.0 with EventID 1310 saying:
Event code: 3008
Event message: A configuration error has occurred.
Event time: 7/20/2016 2:34:28 PM
Event time (UTC): 7/20/2016 11:34:28 AM
Event ID: a59d5b2b449a4b968766e110bc5704a6
Event sequence: 1
Event occurrence: 1
Event detail code: 0
Application information:
Application domain: /LM/W3SVC/2/ROOT/ecp-12-131134880684035632
Trust level: Full
Application Virtual Path: /ecp
Application Path: C:\Program Files\Microsoft\Exchange Server\V15\ClientAccess\ecp\
Machine name: name_here
Process information:
Process ID: 11208
Process name: w3wp.exe
Account name: NT AUTHORITY\SYSTEM
Exception information:
Exception type: ConfigurationErrorsException
Exception message: Could not load file or assembly 'Microsoft.Exchange.Common, Version=15.0.0.0, Culture=neutral, PublicKeyToken=token_here' or one of its dependencies. The system cannot find the file specified.
at System.Web.Configuration.ConfigUtil.GetType(String typeName, String propertyName, ConfigurationElement configElement, XmlNode node, Boolean checkAptcaBit, Boolean ignoreCase)
at System.Web.Configuration.Common.ModulesEntry.SecureGetType(String typeName, String propertyName, ConfigurationElement configElement)
at System.Web.Configuration.Common.ModulesEntry..ctor(String name, String typeName, String propertyName, ConfigurationElement configElement)
at System.Web.HttpApplication.BuildIntegratedModuleCollection(List`1 moduleList)
at System.Web.HttpApplication.GetModuleCollection(IntPtr appContext)
at System.Web.HttpApplication.RegisterEventSubscriptionsWithIIS(IntPtr appContext, HttpContext context, MethodInfo[] handlers)
at System.Web.HttpApplication.InitSpecial(HttpApplicationState state, MethodInfo[] handlers, IntPtr appContext, HttpContext context)
at System.Web.HttpApplicationFactory.GetSpecialApplicationInstance(IntPtr appContext, HttpContext context)
at System.Web.Hosting.PipelineRuntime.InitializeApplication(IntPtr appContext)
>Could not load file or assembly 'Microsoft.Exchange.Common, Version=15.0.0.0, Culture=neutral, PublicKeyToken=token_here' or one of its dependencies. The system cannot find the file specified.
at System.RuntimeTypeHandle.GetTypeByName(String name, Boolean throwOnError, Boolean ignoreCase, Boolean reflectionOnly, StackCrawlMarkHandle stackMark, IntPtr pPrivHostBinder, Boolean loadTypeFromPartialName, ObjectHandleOnStack type)
at System.RuntimeTypeHandle.GetTypeByName(String name, Boolean throwOnError, Boolean ignoreCase, Boolean reflectionOnly, StackCrawlMark& stackMark, IntPtr pPrivHostBinder, Boolean loadTypeFromPartialName)
at System.Type.GetType(String typeName, Boolean throwOnError, Boolean ignoreCase)
at System.Web.Compilation.BuildManager.GetType(String typeName, Boolean throwOnError, Boolean ignoreCase)
at System.Web.Configuration.ConfigUtil.GetType(String typeName, String propertyName, ConfigurationElement configElement, XmlNode node, Boolean checkAptcaBit, Boolean ignoreCase)
Request information:
Request URL: https://localhost:444/ecp/exhealth.check
Request path: /ecp/exhealth.check
User host address: ::1
User:
Is authenticated: False
Authentication Type:
Thread account name: NT AUTHORITY\SYSTEM
Thread information:
Thread ID: 35
Thread account name: NT AUTHORITY\SYSTEM
Is impersonating: False
Stack trace: at System.Web.Configuration.ConfigUtil.GetType(String typeName, String propertyName, ConfigurationElement configElement, XmlNode node, Boolean checkAptcaBit, Boolean ignoreCase)
at System.Web.Configuration.Common.ModulesEntry.SecureGetType(String typeName, String propertyName, ConfigurationElement configElement)
at System.Web.Configuration.Common.ModulesEntry..ctor(String name, String typeName, String propertyName, ConfigurationElement configElement)
at System.Web.HttpApplication.BuildIntegratedModuleCollection(List`1 moduleList)
at System.Web.HttpApplication.GetModuleCollection(IntPtr appContext)
at System.Web.HttpApplication.RegisterEventSubscriptionsWithIIS(IntPtr appContext, HttpContext context, MethodInfo[] handlers)
at System.Web.HttpApplication.InitSpecial(HttpApplicationState state, MethodInfo[] handlers, IntPtr appContext, HttpContext context)
at System.Web.HttpApplicationFactory.GetSpecialApplicationInstance(IntPtr appContext, HttpContext context)
at System.Web.Hosting.PipelineRuntime.InitializeApplication(IntPtr appContext)
In the Queue Viewer I have a lot of emails headed towards certain domains that are stuck with the error:
[{LRT=7/20/2016 2:40:17 PM};{LED=450 4.7.0 Proxy session setup failed on Frontend with '451 4.4.0 DNS query failed. The error was: DNS query failed with error ServerFailure'};{FQDN=correct_fqdn_here};{IP=correct_ip}]
What works:
OWA works from the inside and outside;
Apart from some emails to specific domains (small companies) inbound/outbound emails work from inside and outside of the company.(Tested with a Gmail account, testconnectivity.microsoft.com and received confirmation that emails from some big companies are being received - ex. hp.com)
Apart from the CU9 Update, nothing was changed prior to the update.
Searched the web a lot before asking but nothing helped. I'm guessing most of the issues are because ECP is not working.
Has anyone encountered this issue before and has an idea how to fix it?
Thanks in advance!

Answer 1

After a lot of research I ended up rebuilding the .net folders and AppPool entities in IIS. The main issue being that the IIS AppPools were not pointing to the correct ECP site, etc.
Now it works just fine.