So once that's done and you go back later to update the firmware or database on each scanner, does Sentinel automatically keep the 2 scanners separate? Are there 2 profiles then?
You can set up two, or more profiles in Sentinel. One for the 436, a different one for the 536, maybe another for a trip you regularly take, like to visit relatives or friends in another state.
Regardless of how many 'profiles' you have, the Favorites lists will be the same in all of them, The differences would be more in the settings for which list(s) are downloaded, and how many of them are set to be monitored as well as downloaded. If you have an opening screen message, you might have one for the 436, a second one, with perhaps different wording for the 536. Just remember that any changes you make to a specific Favorites list will be passed along to the profiles devoted to either the other scanner model, or for a specific usage (such as a profile for a trip regularly taken).
Firmware updates are not affected by the profile that is active. Sentinel checks for any firmware updates available for the scanner model connected to the PC & Sentinel. The profile itself is not a part of this at all.