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 ?17.5million 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."