Let's say I cast a card with Cipher from my graveyard with the help of Flashback (provided by Snapcaster Mage). Will I be encoding it on a creature instead of exiling it from the effect of Flashback?
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Yes. Cipher will continue to work as normal.
Cipher exiles the card it encodes.
The relevant part of Flashback is the following replacement effect:
Flashback does absolutely nothing if you exile a card using Cipher because the card is not put "anywhere [other than exile]" when it leaves the stack. Cipher will continue to work as normal.
If you chose not to encode the card, Flashback will cause it to be exiled instead of going to the graveyard.