I've heard this happen quite a lot to people. Your progress isn't lost or reset, it's just a temporary issue.
There's actually a tracked issue regarding this - I've seen that there's potentially a fix that has been found:
"I basically end my session by quitting the game in the stadium. When I start the game back up and travel to San Van its fixed. If I quit the game in San Van and start the game back up all zeros happens pretty much every time."
So basically, they're saying to quit out while in the stadium, or Grom or SUMR camp, and it should display the correct neighbourhood levels when you launch the game again and travel back to San Van. I hope that fixes it for you.