If using Atlas have you tried to talk to Mongo about this? We have the same routine, where we replace Dev from Prod on a regular basis. I believe it’s done at a server level using the toolset that’s part of the Atlas infrastructure.
We have a pretty large replicated cluster and it does not take that long to do the refresh.
At the very least I’d not use JSON as you could lose data typing but use mongodump and import instead unless you have a very good reason not to.
Sorry I’ve not more detail, our DBA team deal with this but I know they do not use dump/restore but do it at a server level and without custom tooling or so I believe.