Ive found that Helium constantly breaks while trying to backup large APKs . So here is a work around which worked for me get a backup of installed apps and data .
1) Backup apk using ES Explorer or equivalent .
2) Backup contents of /Android/obb . ( this is where some apps like games store extra content )
3) Take backup of data using Helium using Web console . May be you can try backing up to device also .. Might work
1) You can either manually install backed up apps using any Android File explorer OR simply use ADB command line (no app installation prompts
adb install -r APk .
To batch install on DOS use
for %i in (*.apk) DO adb install -r "%i"
2) now restore app data using Helium using web console or restoring from device .
3) Restore obb folder contents
This for me was much faster and had lesser failures due to Helium hanging