M0, M2 and M5 instances are shared instances so you cannot upgrade their versions yourself.
Deleting and recreating an M0 instance won’t upgrade it to a higher version, you will just be linked again to the same shared cluster. They will be upgraded to 4.4 automatically in a near future by the Atlas team.
I tested mongoexport 100.1.1 with
- an M0 instance - currently 4.2.9
- an M10 instance in 4.4.0
And mongoexport worked with both. Please double check your command line and your user & IP address as I explained above. It should work for you too.