Repairing MSI's deployed with k1000
Answer Chosen by the Author
A transform is normally for customising an existing MSI and can ONLY be applied at install time. So once the MSI is installed you cannot add the transform.
What settings are you changing?? are you using the Babylon package builder again??
This question is really about how good the Babylon package builder is. I would recommend removing your first package before deploying the new package
MSI's have GUIDs inside that are managed by WindowsInsatller (msiexec), ProductCode, UpgradeCode and PackageCode. You can manage MSI's and updates by using UpgradeCodes and ProductVersion values to maintain installs.
I think the Babylon tool is going to just create a new MSI and it will install over the top of the existing one, meaning if you then remove the first MSI, you will probably break the 2nd MSI. If its a good MSI, it might self repair, but again, I doubt it.
It will be easy for you to test though, just install you 2nd MSI on a machine that already has the first MSI. (do yourself a favour, do a log file of the install)