Correct. My saved data is still there. I just can't, according to a post on Gamefaqs,
Berries stop growing
No more Daily/weekly giveaway of Berries /TMs
No more Secret Base Battles
No More Lilycove Lottery
No More random TV Events
Eevee Happyvolutions locked into Espeon or Umbreon cannot get both
Shoal cave is locked in High or Low Tide meaning you cannot get Shell Bells, and if at high you cannot get Snorunt or the items in the Basement level
Plus the rocket launch count.
Really the only reason I hadn't restarted my file was because I wanted the launch number to get as high as possible. I guess now I can restart to get a bunch of Jirachi.