No, this is not the intended behavior. Usually, only the renamed variable should get lost.
I have checked your project and found the reason why all links get lost in this case. It is a misbehavior of CpStudio that we will need to fix, but it only applies in a special case:
Hard to explain without looking at implementation details, but all elements of the struct instance are removed and added again if the element being deleted has a local property (that is not inherited from the struct definition like MappingName). In other words, if you remove the ExcludeFromMes property before loading the new object version, the problem does not occur. The property is unnecessary anyway (also with the other struct elements), because it doesn't have any effect when it is false.
But of course, also in this case the behavior is not intended, so thanks for reporting!
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