Best way to get the list of XML files
Option Strict  

You should always set Option Strict = On.

Short circuit evaluation  

You should use the AndAlso operator instead of the And operator. By using And both conditions will be evaluated. By using AndAlso the second condition will only be evaluated if the first returns true.  

List(Of FileInfo)  

Instead of returning a List(Of FileInfo) you should consider to return an IEnumerable(Of FileInfo).  

Naming  

You shouldn't prefix your variables like strWorkingPath or lstAllFiles.  

GetFiles() vs EnumerateFiles()  

From the docs  


  The EnumerateFiles and GetFiles methods differ as follows: When you
  use EnumerateFiles, you can start enumerating the collection of names
  before the whole collection is returned; when you use GetFiles, you
  must wait for the whole array of names to be returned before you can
  access the array. Therefore, when you are working with many files and
  directories, EnumerateFiles can be more efficient.


Refactoring  

First we will extract the loading of the file and reading the properties to separate methods and add a private class holding the TypeIndex and Version properties of the xml file.   

Private Shared Function DoesFileMatch(file As FileInfo, index As String) As Boolean
    Dim version As XmlVersion = GetXmlVersion(file)
    Return (version.Version = "0" AndAlso version.TypeIndex = index)
End Function

Private Shared Function GetXmlVersion(file As FileInfo) As XmlVersion
    Return New XmlVersion(XElement.Load(file.FullName))
End Function

Private Class XmlVersion
    Public Property TypeIndex As String
    Public Property Version As String
    Public Sub New(element As XElement)
        TypeIndex = element.Element("TypeIndex").Value
        Version = element.Element("Version").Value
    End Sub
End Class


Next we add an overloaded GetListByType() method which takes a DirectoryInfo and a String as input parameter.  

Shared Function GetListByType(directory As DirectoryInfo, ByVal typeIndex As String) As IEnumerable(Of FileInfo)

End Function


Which we call in our former method like  

Shared Function GetListByType(ByVal typeIndex As Integer) As IEnumerable(Of FileInfo)
    Return GetListByType(typeIndex.ToString(), New DirectoryInfo(GetWorkspaceDir))
End Function  


The overloaded method can then be simplified, using all above, to  

Private Shared Function GetListByType(directory As DirectoryInfo, ByVal typeIndex As String) As IEnumerable(Of FileInfo)

    Dim filteredFiles As New List(Of FileInfo)

    For Each fic In directory.EnumerateFiles("*.xml", SearchOption.AllDirectories)
        If (DoesFileMatch(fic, typeIndex)) Then
            filteredFiles.Add(fic)
        End If
    Next

    Return filteredFiles.Distinct()

End Function


But wait, we can do this a lot more lambda like  

Private Shared Function GetListByType(directory As DirectoryInfo, ByVal typeIndex As String) As IEnumerable(Of FileInfo)

    Return directory.EnumerateFiles("*.xml", SearchOption.AllDirectories) _
        .Where(Function(x) DoesFileMatch(x, typeIndex)) _
        .Distinct()

End Function