What do the upgrade scripts do for the following cases?

Hi,
I have got the compare reports between 9.0 vanilla(Source) and 8.4 copy of production(Target).
it has the following properties.
source---------target--------action-----upgrade
changed-----*changed-------copy-------yes
changed-----*unchanged----copy-------yes
unchanged---*changed------copy--------yes
unchanged----*unchanged--copy--------yes
which means in all the above cases the customizations will be overridden.
I have read somewhere that as a developer i need to look for the following case and re-apply the customizations
source---------target--------action-----upgrade
changed-----*changed-------copy-------yes
my question is that, when we run the 9.0 upgrade scripts on 8.4 copy of production, will it not override the customizations for the following cases?
source---------target--------action-----upgrade
unchanged---*changed------copy--------yes
unchanged----*unchanged--copy--------yes
Please help me,
Thank you.
Edited by: user609854 on Dec 8, 2008 6:20 PM

If you are talking about compare reports during Initial move of Upgrade --Yes , objects from the source will come over and based on user's or you(in this case) have to re-apply them back.At later stages of the upgrade pass you have to re-apply them eventually if you want to opt with old or delivered custom or pure custom psoft objects.

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