Yes, I would say that the notification was from legitimate freebitco.in site, all of my amounts were according to the actual status, the multiply rolls were increasing and decreasing as normal, and the site was refreshed every 1 hour as is normally doing when the timer expires. Everything seemed very legitimate, with the note that this message was there for several days (I would say around 3 or 4 days) and it seemed like the site is legitimate, also, i had the same message also on my mobile app.
I checked in my history stats, my the last deposit and withdrawal to the old address was on 31st March. after that I guess on 1st or 2nd of April was received the notification, and several hours after my unsuccessful deposit to the new P2SH address, the notification was removed and the old address is now showing again.
That's so strange and I don't know why FreeBitco.in would do such a thing. I'm not saying you're not telling the truth, but it seems like something else could be at stake here. You mentioned the notification looked genuine, everything seemed to function normally, and it even appeared on your mobile app. And the notification vanished after your unsuccessful deposit attempt to the new P2SH address, and the old address reappeared. That timing is awfully suspicious and that's concerning if it was a fake.
Also, there don't seem to be any other reports from other users, except for you two.
As I said before, I was active on the site at that time and did not see any notification and my FreeBitco.in deposit address did not change during that period. Only when I requested a new deposit address, the system generated a new address, but it is still a legacy address, and all old, previously generated deposit addresses should work as before.