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I'm attempting up update a Windows 7 (Home) using wsusofflineupdater and it gets frozen at a certain spot:

"Saving system policy registry hive..."

This is a line after:
Installing ..\w61-x64\glb\IE9-Windows7-x64-enu.exe...
Perparing automatic recall...
"Saving system policy registry hive..."

I read that stopping the update when it does this can cause instability in the registry. So I am afraid to cancel.

After looking further into the actual command that issues this, https://svn.wsusoffline.net/svn/wsusoff ... Recall.cmd
It should return an error message if it fails, but it's been running since this morning (+2 hours) and task manager shows no notable activity (CPU, disk and network are nil).

What should I do?

Well, I did a ctrl+c to end the batch process, restarted the PC, re-ran the update and it seemed to go further and complete.

Restarting the process when it was backing up the registry hive had no negative effects.

I installed windows 7 onto my laptop next and tried to do this update again (from a new ISO with freshly downloaded updates).

Same thing. The update process installs IE9, then freezes at the registry hive backup stage.

Stopping the update and restarting it solves the problem.