if I understand right you just need to change your connection and run compare with same pair info. You are right that when you change connection we have to reload all objects and relations so you have to map your tables from scratch. And this is your main problem because you have so many tables which have to be mapped all the time. Is it correct understanding?
Unfortunately only easy way how to change connection is by editing XML file. Specification of connections are in these two elements: SourceConnectionMediator and TargetConnectionMediator.
CurrentDB attribute say what Schema you want to use.
Then there are Connection and ExtraParameter elements.
ExtraParameter is usually empty - usually used for backward compatibility or additional encryption of your password.
Connection specify your connection info. I don’t recommend you editing this info manually. Instead of this you can export your needed connection from your Connection Manager. Connection manager can export your connection(s) directly to XML. Then you can edit this file and you can find your needed connection. Just copy - paste your Connection element.
If you want to use it as a part of your automation script you have to play with it little bit more. Separate your connections to file and then you can use Find-Replace activity.
I didn’t test it with Oracle - Postgres combination but I hope it should be enough. If it doesn’t help then let me know and I will try test it once more on your specific combination.