Odd things happen if you hard reset the phone without unfreezing the backup assistant first. If you are not doing hard reset, phone will work just fine without the backup assistant
i dont believe a factory restore actually erases and reinstalls the os, it just deletes user specific data.
i too have this and some other apps frozen, recently i did a reset and forgot to defrost first. nothing odd happened though ... strange.
i think a better way to do it is to grab rsd lite 4.9 and the sbf then flash the phone from a pc
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