Thoughts on how to fix a depression in the roof

Take a look at the underside of your hood. You will see there are blobs of seam sealer that connect the hood skin to the under brace. This is mostly to prevent vibration but it would work to keep your roof from popping again. You want to use something like seam sealer that has some give to it.
I know you dont want to remove the headliner but this problem is not going away just by popping it back up.