Possible errors when using Web Setup project to upgrade version, that was XCopied

I am using Web Setup project to install Web Site Project(customized version of DotNetNuke). It installs a lot of DLL with meaningless names(like App_Web_42q_drww.dll) into BIN directory.
If user upgrades later to the new version of the project MSI installer seems smart enough to delete old DLLs and install another set of DLLs with different unfriendly names.

The problem happens if site to upgrade wasn’t installed using Web Setup MSI, but was XCopied.The sample scenario is the following:
An administrator  installed web Application into virtual directory MyWebApp1. Then the administrator  made a copy of application MyWebApp1Copy.
On teh time of upgrade he/she decided to apply upgrade directly to MyWebApp1Copy virtual directory. In this case old set of DLLs in BIN is not deleted, but both old and new co-exist. It causes different errors like

Compiler Error Message: BC30456: ‘InitializeCulture’ is not a member of ‘ASP.default_aspx’.

The simplest way to workaround the mess is to rename the web apllication folder and install your application as new.

Related thread : BC30456: ‘InitializeCulture’ is not a member of…