When working with a BizTalk solution, I ran into these issues a lot of times.

• The orchestrations in the referenced BizTalk project may show compiler warnings.
• The changes that are made to the referenced BizTalk project are not propagated on to the referencing project.
• When you edit the orchestrations of the referenced project, XLANG errors are thrown. These errors may disappear after the orchestrations are saved and recompiled.
• After you deploy the referencing project, the local copies of the referenced project’s binaries are deleted.
• After you deploy the referencing project, various errors or warnings occur in Orchestration Designer.

A colleague then metioned about this hotfix - KB 97748. After installing this, the references do work like a charm.

--Sanket