Simple put, it was poor form to de-enable the previous version (2.4.3) of Mystique and NOT put a notice in the Theme Update in the Admin.
I can imagine that hundreds of loyal Mystique users and a few who donated to support the project didn't appreciate expecting a friendly update only to find out that the update not only gutted their site's customization, but didn't allow reconstruction the site without deleting the "update" and installing 3.x.
If the powers to be at WordPress do anything it should be to come up with a rule that says if your update is going to in some way either downgrade, reset or otherwise destroy customizations, that has to be duly noted and that "new" theme needs to upload into a unique directory.
Frankly Mystique growing up to be a Child/Parent theme was overdue, but next time consider alerting those who supported before, not after you update/downgrade a theme.
PS 3.0 is way to buggy to be taken seriously.