You may get below error when you modify your schema and try to deploy this with removing the projects which are making a reference to the schema project.
Error 1 Failed to add resource(s). Change requests failed for some resources. BizTalkAssemblyResourceManager failed to complete end type change request. Cannot update assembly "AS.MS_BTS.EDI_X12.Schema.Outbound.X12_00401_204, Version=1.0.0.0, Culture=neutral, PublicKeyToken=5753f508dd524570" because it is used by assemblies which are not in the set of assemblies to update.
To update the assembly, remove the following assemblies:
AS.MS_BTS.EDI_X12.Partner.Common.Outbound.X12_00401_204, Version=1.0.0.0, Culture=neutral, PublicKeyToken=5753f508dd524570
You may end up undeploying the referenced project from you BT application. A work around which could be used is to take the help of GAC to redeploy the schema assembly and restart the the BIzTalk host instances. Below is the gac util command for the same.
gacutil /if Assemblypath
Coomand:
c:\Program Files\Microsoft Visual Studio 8\VC>gacutil /if C:\SourceCode\Arrowstr
eam\AS\MS_BTS\AS.MS_BTS.EDI_X12._Deploy\AS.MS_BTS.EDI_X12.Schema.Outbound.X12_00
401_204.dll
Results
Microsoft (R) .NET Global Assembly Cache Utility. Version 2.0.50727.42
Copyright (c) Microsoft Corporation. All rights reserved.
Assembly successfully added to the cache
Cheers, Vishnu