The former London Wasp played a central role in the Lions' third Test victory over the Springboks, setting up Shane Williams' second try, having already agreed to join French Top 14 outfit Brive on his return from South Africa.
And with Flutey requiring surgery just one game into life with his new club, the RFU's director of elite rugby Rob Andrew has again spoken out about the difficulties of England's top players plying their trade across the Channel.
"There were a lot of issues around Riki," said Andrew, a Lions tourist himself in 1989 and 1993.
"About whether he should or should not play in the game that led to him having a shoulder injury.
"The reality is that his shoulder would have needed an operation at some point over the next few months.
"There was ongoing dialogue over whether he should play on that particular weekend or whether he should be given another weekend to rehab.
"The medical view was that we would have preferred him not to play that weekend. He wasn't necessarily being put at risk by playing but our preference was that he should be given another week."
And while Flutey is now set to miss his country's autumn internationals against Australia, Argentina and New Zealand, Andrew also has concerns over the international futures of a number of other England stars who moved to France earlier this year.
Of the likes of England caps James Haskell, Tom May, Jamie Noon, Tom Palmer, Iain Balshaw and Jonny Wilkinson, only the latter has clauses written into his club contract ensuring he will be available for all England squad sessions throughout his time in France.
"We expressed very clearly our concerns a year ago as to how moving to France would impact on a player's international selection because we don't have the same level of control with the players we would want," added Andrew.
"We are monitoring very closely just what impact this will have over the course of the season because when we come to next year, the last season before the World Cup, we need to be very clear what issues we might have."