I started up the game today to find that my vault was missing from the list, I didn't let my battery run out or delete anything. It's not so much the vault I'm pissed about it's the money i spent on lunch boxes that have in turn gone with the vault.

check if the files named Vault1.sav ... Vault3.sav are in the Android/data/com.gamesas.falloutshelter/files folder. If they're there and are not 0KB theres still hope. Make a copy of those and resintall, paste them back in there and see if it works.

If the files are missing or 0KB though, I am sorry for your loss.