If they were there one day and gone the next, I would suspect some sort of critter - whether it was an insect or a 4-footed or a 2-footed animal (better known as neighbors).

FataMorgana

Chipmunks will sometimes clear out a planting from a pot they have been using as a lookout station. They do this so their view is not obscured.

If that is the case, moving the pot or placing weighty rocks over the soil might help. However, if something has developed a taste for chives, yours are doomed unless you place them in a safer position or put some sort of repellent on them.

Thank you for the replies, I just wanted to figure out what was taking my chives but it seems that I'll just have to watch them and cover them with netting for now. :) Thank you once again.

Man this JUST happened to me they are gone it’s like they never grew they didn’t wilt and fall over they are literally just gone POOF into thin air