We had a very severe problem recently on our BizTalk environments when building the solution some of the projects lose the reference to other projects in the solution.
We are using BizTalk 2009 Visual studio 2008 SP1 on Windows Server 2008 (SQL Server 2008 though i don't think this has anything to do with the problem)
The references are lost randomly, one moment the solution compiles, or for that mater even when just building a single project, and after a small change (that does not generate an error) the next build VS looses references and can not recognise external components and thus build will fail.
We worked around using file reference and not project reference which seems to respond better but still generates build errors on occasion because of reference loss.
Another detail which is probably worth mentioning is all BizTalk environments are on VPC’s, don't think this should matter.
Searching around we found that this problem was recently raised to Microsoft.
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