So, everything is quite simple, modify your attribute in /models/{name}.settings.json
"location": {
//add this one
"index":"2dsphere"
}
Note: "index":true
adds the regular ascending index, this is why your manually created 2dsphere
was deleted during bootstrap.
Available methods for indexes (only for MongoDB!):
"index":1 // will create regular ascending index
"index":-1 // will create regular descending index
"index":"2dsphere" // will create 2dphere index
Result: