So quick update, using the latest adb I can restore files backed up by Helium. I don't know how to do a batch restore, so far I've only figured out how to do one file at a time.
./adb restore /path/to/backup.ab
Additionally, check this out:
Using whatever old adb is installed on my mac:
~/Downloads/android-sdk-macosx/platform-tools $ which adb
/usr/local/bin/adb
~/Downloads/android-sdk-macosx/platform-tools $ adb version
Android Debug Bridge version 1.0.29
~/Downloads/android-sdk-macosx/platform-tools $ adb devices
List of devices attached
Using the newest version of adb downloaded yesterday:
~/Downloads/android-sdk-macosx/platform-tools $ which ./adb
./adb
~/Downloads/android-sdk-macosx/platform-tools $ ./adb version
Android Debug Bridge version 1.0.31
~/Downloads/android-sdk-macosx/platform-tools $ ./adb devices
adb server is out of date. killing...
* daemon started successfully *
List of devices attached
*************** device
(I blanked out the serial number since I can't remember if that's sensitive or not)
I think it's clear that an older version of adb doesn't recognize the phone, for whatever reason, so this is likely the problem.