Barbados-born Archer -- described by England all-rounder Ben Stokes as the most "naturally-gifted" bowler he has seen -- became eligible for England earlier this year.
Previously, players who entered the UK after turning 18 needed to live in the country for seven years to be eligible for England, but the ECB reduced that to three years. Archer arrived in 2015.
Woakes told BBC Sport that England, the top-ranked one-day-international team, have become close under captain Eoin Morgan as they prepared for the World Cup which gets underway in England at the end of May.
"It probably wouldn't be fair, morally, but at the same time it's the nature of international sport," said Woakes.
"If he was to come in and someone was to miss out, it would be extremely unfortunate.
"We've been a tight-knit group for the last two to three years, played some really strong cricket, won a lot of series.
"I wouldn't want to see any of my mates and team-mates miss out." But the all-rounder insisted that England would remain focused on the job at hand should Archer get a call-up.
"I don't think it would disrupt the team, because everyone would find a way to move on and we're trying to win a World Cup for England. That's the bigger picture," added the 30-year-old.
Archer, who is playing in the IPL for the Rajasthan Royals, has appeared in just 14 one-day matches as a professional, but England coach Trevor Bayliss has said the all-rounder will feature in the ODIs against Ireland and Pakistan in May.
Other England pace bowlers have also expressed doubts. David Willey said in March he did not know "whether someone should just walk in at the drop of a hat because they're available".
Mark Wood said last week that selecting Archer risked changing the "dynamic" of the side.
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