Release 4.6.0.15 was a stop release (read here). This means a device must be updated to 4.6.0.15 before proceeding to 5.0.0.
The GUI should be used for updates as it “knows” the next mandatory release. In your case, the phone had 4.6.0.13. The GUI should have proposed 4.6.0.15 - it wouldn’t let it go directly to 5.0.0. But there was something wrong with your phone.
If the command line has to be used for updates then you have to ensure that all stop releases are installed. No shortcuts to the latest release!
# starting from 4.6.0.13
ssu re 4.6.0.15
version --dup
reboot
ssu re 5.0.0.55
version --dup
reboot