I guess I haven't explained my requirement clearly so deleted the original question and asking again. Apologies for that !!
Basically, I have a folder containing close to 3000 files (majority of them are dlls taken from the projects that we constantly make changes to). Of these 3000 files, some needs to be untouched upon upgrades (I will use your "permanent" flag which I just tested and worked. thanks for that).
For the remaining dll files. I need a way where I can push the newly built ones as an msi package so that they are updated in the master folder on the fields without uninstalling. I couldn't take patch route as my company wants to see only one entry in the control panel > programs with latest version of the product (just like any other usual software like notepadd++ or ccleaner etc) but still updates the newly enhanced dlls.
Sometimes, we send only 1 dll to the field and most of the times we have to send them in hundreds. So a major upgrade which not only updates (even replacing is fine) the existing dlls is what am looking for. The option "afterInstallExecute" is not working for me as it is deleting the dll although I am changing the version and sending.
<MajorUpgrade Schedule="afterInstallExecute" AllowDowngrades="no" DowngradeErrorMessage="A newer version of $(var.ProductName) is already installed. Setup will now exit." />