Full Outer Join not working as expected
Firstly, I'd encourage you to read the blog post Be Careful When Mixing INNER and OUTER Joins.  


  If you use Derived Tables (or nested joins) the way you'd use
  parenthesis in a math or boolean equation to express your logical
  order of precedence, you can make your code cleaner and more readable
  and you can ensure that you get back the exact results you intended.


I don't know if this will solve your problem, as you did not post any table definitions or sample data, but I'd try changing your query to encapsulate the inner join into a derived table and then join the derived table using the FULL OUTER JOIN.  Here is an example (not tested):

SELECT DISTINCT [ij].[Artikelnummer]
    ,[ij].[Bezeichnung1]
    ,[ij].[AuspraegungID]
    ,[ij].[USER_SkuDe] AS [Parent SKU]
    ,[AV].[USER_SkuDe] AS [Varianten SKU]
FROM (
    SELECT [A].[Artikelnummer]
        ,[A].[Bezeichnung1]
        ,[A].[USER_SkuDe]
        ,[S].[AuspraegungID]
    FROM [dbo].[KHKArtikel] [A]
    INNER JOIN [dbo].[LBSysStock] [S]
        ON [S].[Artikelnummer] = [A].[Artikelnummer]
    ) ij --inner join
FULL OUTER JOIN [dbo].[LBSysArtikelVarianten] [AV]
    ON [ij].[AuspraegungID] = [AV].[AuspraegungID]
        AND [AV].[Artikelnummer] = [ij].[Artikelnummer]