Central midfielder Scowen, 23, and forward Watkins, 26, have been offered new deals but are waiting to see what other options they have in the summer. After good first Championship seasons, both are likely to have plenty of admirers able to offer more money than Barnsley.
Heckingbottom told the Chronicle: "I have spoken to Josh and Marley and they know how much they are loved and wanted at Barnsley. But we know that, financially, they may be able to get a better deal from another club and they are waiting to see what is out there.
"It's not definite that they will leave us but we can't be held to ransom and we can't delay our plans by waiting for them. I am planning without them then, if we get them, it is a bonus."
Whatever happens with Scowen and Watkins, Heckingbottom is expecting to have to bring in at least ten players before next season. He said: "It will depend on who leaves, but I would say it will definitely be into double figures. "It will take a hell of a lot of work. I'd like to get some deals done early but we aren't close to any at the minute."
The head coach still expects all six loan players not to play for Barnsley next season. Adam Armstrong has already returned to Newcastle United, as he cannot play against them in the last game of the season on Sunday. The same will happen with Leicester duo Callum Elder and Matty James, Celtic's Saidy Janko, Liverpool's Ryan Kent and Everton's Gethin Jones – none of whom Barnsley are expecting to bring back.
The Reds are also braced for bids for their best players, with captain and star centre-back Marc Roberts – having been linked with Premier League clubs all season – currently the most likely to follow Sam Winnall, Conor Hourihane and James Bree who were all sold in January.
Heckingbottom is set for meetings with all of the out-of-contract players next week. Those players include Aidy White, who has struggled with injuries during his two years at Oakwell, as well as several youngsters such as defenders Callum Evans and Jack Cowgill.
Barnsley have an option to extend Ryan Williams' contract into a third year or to release the midfielder who has made just five league starts since signing in 2015. They may also look to offload players such as Cole Kpekawa, who signed a three-year deal in August but has been frozen out of the first team picture since October.
The Reds are still yet to appoint a new chief executive following the departure of Linton Brown almost four months ago on January 13. They were given a boost when owner Patrick Cryne made his first appearance at a home game since the announcement that he is battling terminal cancer, in Saturday's 1-1 draw with Burton Albion.
The Reds are 14th in the Championship with 58 points, which puts them ten clear of the relegation zone and 19 off the play-offs, which they were four points away from in January before a run of just two wins in 17 matches. Barnsley are unlikely to drop down any places, with only Wolves capable of catching them but needing a five-goal swing in goal difference, while they could still finish in the top half by overtaking Cardiff City and Aston Villa.