One way would be to define a "outer" schema and import schemas for the different versions you need to support. The "outer" schema will offer a choice
block containing references to your imported version schemas.
If you need to add the next version you just have to import a new schema and add it to the choice
.
The hard part of course is how you can determine how to process different versions. Maybe the simplest way would be to create a map for every dedicated type you need to handle. On the other hand you could extend a "latest-and-greatest" internal message type and decide based on message content.
"outer" schema
<!-- language: xml-schema -->
<?xml version="1.0" encoding="utf-16"?>
<xs:schema xmlns:ns0="http://ACME.Version_001" xmlns:b="http://schemas.microsoft.com/BizTalk/2003" xmlns="http://ACME.Outer" xmlns:ns1="http://ACME.Version_002" targetNamespace="http://ACME.Outer" xmlns:xs="http://www.w3.org/2001/XMLSchema">
<xs:import schemaLocation=".\version_002.xsd" namespace="http://ACME.Version_002" />
<xs:import schemaLocation=".\version_001.xsd" namespace="http://ACME.Version_001" />
<xs:annotation>
<xs:appinfo>
<b:schemaInfo standard="Flat File" root_reference="Root" />
<schemaEditorExtension:schemaInfo namespaceAlias="b" extensionClass="Microsoft.BizTalk.FlatFileExtension.FlatFileExtension" standardName="Flat File" xmlns:schemaEditorExtension="http://schemas.microsoft.com/BizTalk/2003/SchemaEditorExtensions" />
<b:references>
<b:reference targetNamespace="http://ACME.Version_001" />
<b:reference targetNamespace="http://ACME.Version_002" />
</b:references>
</xs:appinfo>
</xs:annotation>
<xs:element name="Root">
<xs:annotation>
<xs:appinfo>
<b:recordInfo structure="delimited" sequence_number="1" child_delimiter_type="hex" child_order="postfix" child_delimiter="0x0D 0x0A" />
</xs:appinfo>
</xs:annotation>
<xs:complexType>
<xs:sequence>
<xs:choice minOccurs="1">
<xs:element ref="ns0:Version_001">
<xs:annotation>
<xs:appinfo>
<b:recordInfo sequence_number="1" structure="delimited" />
</xs:appinfo>
</xs:annotation>
</xs:element>
<xs:element ref="ns1:Version_002">
<xs:annotation>
<xs:appinfo>
<b:recordInfo sequence_number="2" structure="delimited" />
</xs:appinfo>
</xs:annotation>
</xs:element>
</xs:choice>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:schema>
Imported schema "Version_001"
<!-- language: xml-schema -->
<?xml version="1.0" encoding="utf-16"?>
<xs:schema xmlns:b="http://schemas.microsoft.com/BizTalk/2003" xmlns="http://ACME.Version_001" targetNamespace="http://ACME.Version_001" xmlns:xs="http://www.w3.org/2001/XMLSchema">
<xs:annotation>
<xs:appinfo>
<b:schemaInfo standard="Flat File" root_reference="Version_001" />
<schemaEditorExtension:schemaInfo namespaceAlias="b" extensionClass="Microsoft.BizTalk.FlatFileExtension.FlatFileExtension" standardName="Flat File" xmlns:schemaEditorExtension="http://schemas.microsoft.com/BizTalk/2003/SchemaEditorExtensions" />
</xs:appinfo>
</xs:annotation>
<xs:element name="Version_001">
<xs:annotation>
<xs:appinfo>
<b:recordInfo structure="delimited" child_delimiter_type="char" child_order="infix" rootTypeName="Version_001" child_delimiter="," />
</xs:appinfo>
</xs:annotation>
<xs:complexType>
<xs:sequence>
<xs:element name="Col1" type="xs:string" />
<xs:element name="Col2" type="xs:string" />
<xs:element name="Col3" type="xs:string" />
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:schema>
Imported schema "Version_002"
<!-- language: xml-schema -->
<?xml version="1.0" encoding="utf-16"?>
<xs:schema xmlns:b="http://schemas.microsoft.com/BizTalk/2003" xmlns="http://ACME.Version_002" targetNamespace="http://ACME.Version_002" xmlns:xs="http://www.w3.org/2001/XMLSchema">
<xs:annotation>
<xs:appinfo>
<b:schemaInfo standard="Flat File" root_reference="Version_002" />
<schemaEditorExtension:schemaInfo namespaceAlias="b" extensionClass="Microsoft.BizTalk.FlatFileExtension.FlatFileExtension" standardName="Flat File" xmlns:schemaEditorExtension="http://schemas.microsoft.com/BizTalk/2003/SchemaEditorExtensions" />
</xs:appinfo>
</xs:annotation>
<xs:element name="Version_002">
<xs:annotation>
<xs:appinfo>
<b:recordInfo structure="delimited" child_delimiter_type="char" child_order="infix" rootTypeName="Version_001" child_delimiter="," />
</xs:appinfo>
</xs:annotation>
<xs:complexType>
<xs:sequence>
<xs:element name="Col1" type="xs:string" />
<xs:element name="Col2" type="xs:string" />
<xs:element name="Col3" type="xs:string" />
<xs:element name="Col4" type="xs:string" />
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:schema>
(some default attributes omitted for readability)