I've seen Kies firmware updates wipe the phone too.
Sorry but are you telling us you don't backup and restore such things?
As to the upgrade problem I see that a lot. Now that I've done it a dozen times it's very unpopular what I discovered. That is, "works fine for me." So in a dozen times, it went off without a hitch on our laptops but something is amiss on the owner's PC.
What I'm encountering are folk that demand Samsung fix their PC when this happens. I'm unsure how this will play out since as we are well past the years where folk were expected to troubleshoot Windows and we now expect these things to just work.