How to avoid unregistering of mscoree 2.4 during 2.0 installation?

Question

I've an application that depend on a reference to mscoree 2.0 (from .net 2.0-3.5). I know that it isn't a good practice, but I've to live with it for now.

The app is installed with standard msi (generated by Visual Studion setup project). My issue is that I've .net 4.0 on the box with mscoree 2.4 installed and each time I'm installing my little app the mscoree 2.4 get unregistered and I need to repair .net 4.0 installation in order to get it back in order.

Do anyone faced similar behaviour with .net COMs? Is there an easy way / workaround to avoid mscoree 2.4 unregistration?