Hello @coloradodev 
I would like to inform you that we’ve just released version 2.9.0 of DevKinsta as announced here .
I’ve also just upgraded my DevKinsta from 2.8.0 to 2.9.0 version (Note: I’m on Linux laptop - based on Ubuntu 18.04.5).
After that I tried to reproduce the reported issue by pushing/uploading partial sub-folder (and its files/sub-folders) from my local site in DevKinsta to my Staging site on Kinsta server.
Once completed, I then compared the uploaded subfolder (and its files/sub-folders) on both my local site and on the server side, and they all looked the same (so far I didn’t see any missing files/sub-folders).
Could you please try to re-test the same from your local end (Windows 10 Pro + WSL2) with this new DevKinsta 2.9.0, and see if the issue resolved now?
Cheers,
Agus