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New Zealand-born Stokes hasn't played for his country since September, when he was arrested in Bristol.
He is due to appear at magistrates' court on February 13 charged with affray.
That date clashed with the 26-year-old all-rounder's planned comeback in a Twenty20 against the Black Caps in Wellington.
While the England and Wales Cricket Board is hopeful he will be clear to play the five-match ODI series which starts on February 25, officials are awaiting clarification of the legal process.
His travel arrangements are yet to be confirmed and it is possible he will link up with the rest of the squad separately.
England's decision to name Stokes with a caveat beside his involvement follows a familiar pattern dating back to the Ashes, with the player selected but ultimately deemed unavailable for both the test and ODI series in Australia.
An ECB board meeting decided he was once again available to represent England following his charge last month.
Elsewhere, selectors have named an almost identical 50-over squad to that that which beat Australia 4-1 in recent weeks.
Joe Root, Moeen Ali and Chris Woakes all take their places after being granted a rest from the forthcoming T20 tri-series against Australia and New Zealand.
Eoin Morgan (capt), Moeen Ali, Jonny Bairstow, Sam Billings, Jos Buttler, Tom Curran, Alex Hales, Liam Plunkett, Adil Rashid, Joe Root, Jason Roy, Ben Stokes, David Willey, Chris Woakes, Mark Wood.