@WyrdFish,

Thanks for the reply. 

As MSI won't rewrite the unversioned file if it is modified, I have taken
the following approach as a workaround. During install, my custom action
writes some valus to web.config. During upgrade, installer wouldn't replace
this web.config file as it is unversioned and modified. And inturn my custom
action again writes the same values into the web.config file thus creating
duplicated values in web.config.

To solve this I am moving web.config to separate location and thus during
upgrade, installer detects that the file is missing and copies that file.
After that I will replace this new file with the existing one. Thus way I
can avoid creation of duplicate keys with my custom action during upgrade.

Do you think this might have caused the issue?

@Pally Sandher

I have tried using XmlConfig but in the following manner. When I am
installing freshly, that package uses XmlFile, but I have replaced that with
XmlConfig in upgradeable version package and tried upgrading. Still I got
the same issue during uninstall.

I will try using XmlConfig in both the packages and check if that works.

Sainath A.

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