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I have a model with an object 'A' which references an object 'B'. I delete 'B', I add an object 'C' and I reference it from 'A'. EMFCompare correctly find that 'B' has been deleted and 'C' has been added but it doesn't detect that the reference 'A' to 'B' has changed into 'A' to 'C'.
Created attachment 202166 [details] A picture as example
Please provide us with the example models you've used for this, especially if they have IDs defined. This will allow us to test this more accurately.
Created attachment 202207 [details] The original UML model (technical ids)
Created attachment 202208 [details] The modified UML model (technical ids)
This has been fixed since on master and can no longer be reproduced.