"Swap Apps Devices" works by swapping one device's hub/database-assigned ID with that of another. (By this, I mean the number you see in the URL but not really anywhere in the UI; thisis is distinct from the Device Network ID.) There's nothing a specific app should need to do when this happens, nor would most apps really need to know or care (except as below), whether rules or other apps. If you think you notice something, I suggest reporting it so it can be investigated. But I don't see any issues with this.
The exception, of course, is when the devices aren't exactly the same and one app depends on a capability, command, or attribute that one device/driver may expose while another doesn't. This is the same pickle you can get yourself into if we leave the new "swap" feature out of the picture and, say, just change the driver on the device yourself. You'd want to be certain the devices are either truly the same (e.g., same driver) or at least implement the same capabilities or the specific one(s) you need for the app(s) that are using them.
Also, for the Hubitat historians, I think the first version of Rule Machine for Hubitat just created "Rule" apps, presumably implicitly something like 2.0; then the one after was "Rule 2.5." The 1.x versions were presumably just on SmartThings. 
(But that history I don't remember as well...)
