I think I understand what you are describing. I think we have a similar setup. 
We have a lot of solutions that follow this pattern (please let me know if this 
does not accurately describe what you are trying to describe):

The solution has one or more assembly projects, each with many file references 
for dependencies.
The solution has one project for the windows service host with one or more 
project references to other projects in the solution and file references to all 
required dependencies.
The solution as one wix project for the msi with a project reference to the 
windows service host project. In the wix source you use 
$(var.WindowsServiceHostProjectName.TargetDir) to locate all of the files that 
need to be packaged.

I believe this is a convenient way to locate all required files for your MSI as 
the windows service host project requires all of these files for dev testing 
anyway.

Edwin G. Castro
Software Developer - Staff
Digital Channels
Fiserv
Office: 503-746-0643
Fax: 503-617-0291
www.fiserv.com
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> -----Original Message-----
> From: Brownfield, Cory [mailto:cbrownfi...@aeci.org]
> Sent: Tuesday, November 27, 2012 6:51 AM
> To: wix-users@lists.sourceforge.net
> Subject: [WiX-users] Project reference question
> 
> My team has decided to add only the top-level project reference to the WiX
> project in each solution.  We typically have simple builds where each solution
> has one WiX project that builds a single MSI.  So if we have a service 
> solution,
> we will be adding a single project reference to our WiX project for the
> Windows Service Host.  Since that project gets a copy of all other project and
> library DLLs when built (we will be making sure of that), we will just be
> referencing the DLLs from this top-level build directory in the WiX script.
> 
> This seems to be wrong, but I can't come up with a compelling argument as
> to why.  What problems might be introduced by using this method?  If this is
> a perfectly valid method, let me know.
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