Hey Saqui, the weird bit here is that one did go back. Traditionally the Special Gold Mine, like the Arctic Iron Mine, Industrial Mines, Gem Pits and Packed Wheatfields (and Pumpkin Cemeteries) do not go back to the star. Ages ago there was a mad bug with Artesian Wells but typically they also do not return to the star.
They usually all have the "You will get back these resources:" tooltip and do not have the 'return to star' yellow *splat* in the building info.
The Endless Copper Mine (20k gems in the merchant and not tradable) is the exception to the general rule of fancy mines, it has the *splat* and does return to the star:
To sum up: Looks like TheVictorious hit a lucky fluke-bug, or (and this doesn't seem as likely somehow) BB have something up their sleeves. Until/if that's confirmed I'd be very very very cautious about demolishing most fancy mines.
EDIT: Personally I think TheVictorious should still get a replacement for the 2nd vanished one, not because that's usual but for braving the dangers of experimenting when things go hinky and unclear.