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What the programming (battery registration) does is reset adaptations for the charging cycle. The car needs to know the battery specs (approximate) and age. As the battery gets older it charges less efficiently and is therefore given more power in the charging cycle. In theory, you would damage the battery and overcharge it if you had a new battery in there getting extra voltage because the car thinks it is old.
What that means is you would probably not want to put your old OEM battery back in after registering your new battery if it doesn't work, because I don't believe you get a choice of saying I changed my battery to an old one, please charge it harder. You probably DO want to register the new battery right away since it is presumably smaller and should be charged differently.
EDIT: I see you mean just to reconnect old one without having the new one installed in the interim. That is okay, no need to register as it will still have the adaptations for that battery.
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