> Should I be manually changing the product code of each instance
every time? Or should the base product code be static also? Or ought it not
matter?

Follow the Windows Installer documentation guidelines as for when to change 
your PC:
http://msdn.microsoft.com/en-us/library/aa370579(v=VS.85).aspx .  There are 
some cases where changing the PC on every build might be justified; I'm not 
sure what your servicing strategy is...

Also, review the guidance regarding the UpgradeCode:  
http://msdn.microsoft.com/en-us/library/aa372399(v=VS.85).aspx


> In summary, my question is how should I author the installation package and
how should I run it in order to upgrade only a single installation instance
(when there are multiple installed instances)?

Windows Installer's "Upgrade" table has a field called 'ActionProperty':  
http://msdn.microsoft.com/en-us/library/aa372379(v=vs.85).aspx

WiX allows you to define that property name through the "UpgradeVersion" 
element's attribute called "Property".  WiX documentation here notes:
"When the FindRelatedProducts action detects a related product installed on the 
system, it appends the product code to the property specified in this 
field....After the FindRelatedProducts action is run, the value of this 
property is a list of product codes, separated by semicolons (;), detected on 
the system."

Armed with all of this information it should be clear why all of your existing 
instances are being removed.  Thus, one rather simple way of removing only the 
instance you care about is to author a custom action to manipulate the value of 
your 'ActionProperty' after 'FindRelatedProducts' has executed.  You could 
totally clear it out (install a new instance), or set it to the instance 
product code you wish to have 'upgraded'.

There are other things to consider, but this should get you headed in a more 
proper direction.





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