I checked the configuration of this site, and when the asteroid disappeared it's by design. When you enter the site, there is a very good chance that the asteroid will despawn. Hence mining it is rather tricky.
Since this is normal game mechanics we are unfortunately not able to reimburse you for this asteroid. I'm sorry about that.
EVE Online Customer Support
A bit cryptic, and seems to point to some sort of radar/mag site function where you need to keep a character on grid or it disappears. I am requesting clarification and will share.
Also, I am timestamping that our grav site respawned all the ore today, to see if the timer will also be reset along with the ore. Will post a response when I find out.