InstallAware

An upgrade first runs the (Un)Install MSI Setup to uninstall the previous version.

If you happen to try to cancel once that plug-in is finished (it's installing the new version). The new install is correctly rolled-back but the uninstall is not!

The result is that the user is left no application installed anymore. Is there any fixes for this?

If Windows Installer has moved to the actual uninstall phase by the time you have clicked Cancel, you will not be able to abort. Otherwise, you will be able to cancel normally.

This is not a bug. If you are removing an old version and the removal is already complete, you cannot reasonably expect a roll back of that removal. There is no undo for an uninstall with any product in the world.