I just setup a void miner in the end but forgot to get a flux point for power. When I tried to go back the miner and the waystone I left there was deleted but the cobble tower I also built was still there. I don't know if this was a one time thing or a big bug but this made me lose a lot of resources.

What I did was go to the end.
Go to the out lands
Build it in a chunk with waystone
Leave
And try to go back with the waystone
If can't with waystone just go the original way.

Again I don't know if it will happen again but just in case