i'm wondering why sonar is even "re-selecting" anything - the selection was made before the process - it's like sonar's making new versions of the clips/selection and replacing the originals with those, rather than changing the existing clips/selection in place - that could explain the behaviour, but it's all speculation without access to the code ;-)
whatever, the fact that the selection is changed is unintuitive and unexpected, so at least you could say it's a ux or ui issue