There are numerous bugs in the "media device" drivers for both Mac and Windows. These bugs can cause files not to appear and therefore not be copied to your computer. If you power off, then power on your device, than, at least for a short period of time, the media device driver seems to behave itself.
If you suspect that not all of your files are being copied, you can use the Android app, OI File Manager, to zip up the odk directory, then copy that one file over.
I found this hint at ODK Briefcase -- no files show up? - #2 by Mitch_S I'll update the docs so it's more visible to users.
Looks like this warning in the docs already! https://docs.opendatakit.org/briefcase-using/#pulling-forms-from-collect