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It seems there's a problem with Schema identification when reassigning patch numbers.
If you have multiple schema items within a patch and extract the patch for multiple schemas, all is well.
But if you reassign method items from multiple schemas to a new patch, the schema is lost on lower schema items. Now, although the items appear in the new patch, extracting them will miss any items from lower schemas. Clicking on such an item in the patch, clearly shows the wrong schema.
If this patch is active, and you change such an item, the schema still appears incorrect. However, if you extract the patch for multiple schema, you will get the item correctly extracted.
To reproduce:
Set patch 1 as active.
Change method 1 in Schema 1.
Change method 2 in Schema 2 (a lower schema).
Extract patch 1 for all schemas. All is well.
Reassign both items to patch 2.
Extract patch 2 for all schemas. Oops, method 2, schema 2 is not included.
Display the patch summary and click on method 2. The wrong schema (1) is displayed.
Again change method 2 Schema 2 in the active patch 2.
Extract patch 2 for all schemas. Method 2, schema 2 is included.