The references included in the SitefinityWebApp point by default to the project's bin folder. When you rebuild the project the contents of the bin folder are erased, and theses references are also deleted from the project references. However, you can easily avoid this if you point your project references to another location, and thus whenever you rebuild the project they won't be wiped out, since it doesn't depend on the contents of the bin folder anymore.
All the best,
the Telerik team
Do you want to have your say in the Sitefinity development roadmap? Do you want to know when a feature you requested is added or when a bug fixed? Explore the Telerik Public Issue Tracking
system and vote to affect the priority of the items