Updating the pot is fine. Just don't update the po files as this adds false translations and exceptions.
that is hard manual work... :-( i updated the po and get lots of fuzzy stuff.The update script deletes old entries and adds the new ones. The only problem is if it adds fuzzy to the new one. So, run the script, then diff the de.po and verify the changes are OK. When satisfied commit de.po. You can even make the script just do your po.
But the point is to only commit po files you have verified and test... rather than let an automated process add crashes to what was previously working.