MySQL: Why is this UPDATE query so incredibly slow?
Why don't you just build a temp table and use the results to update. This is bad form. It's got to build the Subquery first, then assemble that in the WHERE Clause, then it's going to update every record to find a match.

Instead just INNER JOIN to a temp table that does the first part, or a CTE if you're using SQL Server and can't have a multi-step process.

WITH SkuList AS
(
SELECT DISTINCT sku FROM (
  SELECT name,size,colour,sku,quantity,price FROM ActiveProducts
  UNION ALL
  SELECT name,size,colour,sku,quantity,price FROM XMLImport
) tbl
GROUP BY name,size,colour,sku,quantity,price
HAVING count(*) = 1
ORDER BY name,size,colour,sku,quantity,price
)
UPDATE ActiveProducts ap INNER JOIN SkuList xml ON ap.sku = xml.sku
SET
  ap.name = xml.name,
  ap.size = xml.size,
  ap.colour = xml.colour,
  ap.instock = xml.instock,
  ap.quantity = xml.quantity,
  ap.price = xml.price,
  ap.updated = 1