I have not heard anything specific about this, but might have missed that since I have not used Jet Blue Points.
If Jet Blue has an existing agreement with Alaska, then its probably safe. If not, then this option may disappear once they integrate the two programs.
So far they have announced the Hawaiian card from Barclays will go away. You won't be able to move miles from one person to another for free like current Hawaiian card holders can. Also they will be removing the options for transfers from bank points currency, i.e. the current option to transfer Amex points to HA miles.