Jos,
Yes, in Beta 1, if you install v2.0, all your apps in IIS will be upgraded to v2.0, and you have to manually run "aspnet_regiis -s" on those apps that you want to keep as v1.1.
We're looking to make this better - to install the new version without upgrading existing websites to v2.0.
One known area that is "broken" when upgrading to v2.0 is debugging existing apps using VS 7.1, because you can't debug v2.0 apps with VS 7.1 (you have to use VS 8.0). Did you have something else that was broken, that did not involve debugging?
Thanks,
Leonid
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