The pair moved to Ewood Park on temporary deals in January and Kean had hoped to negotiate prices with their parent clubs for summer transfers.
Blackburn want to re-sign Paraguay striker Santa Cruz, 29, from Manchester City two years after selling him to the Eastlands outfit for £17.5 million while American midfielder Jones, also 29, is contracted to Schalke.
Kean told the Lancashire Telegraph: "We tried to fix a price for Roque and the same for Jermaine because we thought they would do well but we couldn't fix a price.
"We were confident they would do well but obviously if they do really well now then the price becomes too much.
"We tried to get a price fixed but the parent club wouldn't allow that and we just have to get on with it.''