Question for the Zen gods...

Is there any reason one can not replace an MSI that an app points to?
For some reason I remember long ago someone saying it's bad.

Example. The 15th iteration of Quicktime comes out for this year...
Can you just copy the new MSI over the old one without having bad things
happen to the app? I always create new apps and have to create all the
properties again etc, etc, etc.. It would save a lot of time if I could
just replace the MSI.

Just curious