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When generating source from a UML diagram it's not always practical to generate the source markers for merging/synchronisation. So when you amend the source and then Reverse Engineer it back, any associations, compositions or aggregations you had are lost. Could it be possible to do an intermediate sync level, where the source is merged with the existing UML element. example: If you create a composition in UML, then generate the source code. Then you change change the source (but leave the composition name as when it was generated). Then when you reverse engineer the code, it merges back, not removing the associations et cetera.
This should have been put in as an Enhancement.