I received this message when starting the sim today, probably because the sim hung during my Carribean Dominican Republic / Haiti Bush Trip yesterday, so I had to kill the application in Task Manager. Subsequenlty, the sim hung every time I tried to load the Bush Trip, so I also had to recreate the RollingCache in order to get the flight to load again:
Most people, including myself, have no idea what data is being stored in the cloud vs on my device (PC), so the screen above is not really helpful. How can I make an informed decision if I have no idea what data is different?
My request is that this GUI window include information that identifies the data. I’m guessing that it is some or all of my profile data, but it might be something else entirely!
[I chose “cloud”, by the way, & hoped for the best!] 
Hi, this is a standard Xbox gaming message. You also get it on Console sometimes for various games, not just MSFS.
Unfortunately the only way you can currently work out which one to use is with an educated guess.
i.e. In the past I’ve had this message, I knew I hadn’t flown on MSFS anywhere else so I chose the (newer) option
Your “Profile” which is everything stored inside your profile (hrs, adventures, controller profiles etc) are stored on the PC and when MSFS shuts down okay, the local copy updates the cloud copy.
Guess you had a crash or something because it’s saying your two copies are out of sync. Chances are picking either should be okay, unless you made loads of changes just before crashed or failed the update.
What you do not want is a corrupt profile, because then you have to delete the Cloud based profile and create a fresh one, losing in the process all your MSFS history, hrs and controller configurations.