The mekanism Digital Miner has been disappearing for many players over a couple of weeks now. All the cases I know have been on servers. Unfortunately no logs. https://github.com/whatthedrunk/allthemods/issues/90
Hopefully this little information can help.

I'm unable to reproduce this. Make sure the server admin has not disabled Digital Miners in the config.

This just happened to me too was after I went to nether came back no miner, and it wasnt stolen as I am doing single player