Disclaimer: I have a Rytm, not an A4. I presume the kit system works the same way on both.
When you do this, you’re changing the current state of Kit 1 until you save the Kit as Kit 2. Copying a Pattern keeps the original Pattern-Kit association until you save the new kit.
Starting a new blank Pattern also, temporarily, assigns the last used Kit to the new Pattern, so making changes to the Kit in this new Pattern will also affect the Sounds in the last used Kit, until you save a new Kit.
You should be able to get back the old, unchanged, state of Kit 1 by returning to the original Pattern and using the reload kit commands (e.g. [No]+{Play/Kit] on the Rytm). This might not work after you’ve saved the new Kit 2… I don’t remember.
The design decision on the Analogs is that new Patterns are treated as part of the same “song”–i.e. they have the same sounds–as the last Pattern you worked on. In a way, because the Analogs have Song Mode, this makes sense from an overall design perspective. If you want your Patterns & Kits to behave like the Digi range (Kit per Pattern), save your new Kit as soon as you start work on a new Pattern. The Digi range does not have Song Mode, so the design feels “symmetrical” to me.