[wix-users] Upgrade Scenario Issue

[Ven H]

I have a situation. There is an existing MSI, which has some features and
components for installing application and database. It also has lots of
custom actions written in vb script. This MSI doesn't seem to be following
best practices. This MSI installs files, deploys DLLs into GAC, registers
some COM components into registry, creates an IIS website and some
application pools and also creates some databases and tables and so on.
Unfortunately, this MSI has been running at their end customers for the
past few years. Now, my client has understood that it has lots of issues
and hence needs to be rewritten.

 As part of the rewrite, I am using 2 features only, one for application
and the other one for db. Also, I am using the same upgrade code of the
existing MSI. Now when I try to upgrade the existing database only using my
New msi, it is partially affecting the application also. I said partially
because, even though I want to upgrade only the Database, it is partially
uninstalling the application also (It is deleting the files and folders,
but not uninstalling the app pools and so on). How can I avoid deletion of
files during the upgrade. Please help.