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the only time you might need to be physically in US is while filing extension. you should be present in US on the day of filing extension. otherwise your petition (i797b) would get approved in consular mode. only headache with getting a petition in consular mode is that your company won't be able to extend their i9 up to extension date until you get a new stamp, enter US and give them your new i94. if this happens and if consulates are closed, it might affect your employment. if you get i797a aka a petition with i94 attached to the bottom, they would directly be able to extend your i9. so just be cognizant of this alone.