With the 16:00GMT deadline imposed by the football authorities having expired for both clubs to have passed into new ownership Bury appeared to be in the deepest trouble.
Should either be expelled they would be the first FA Cup winners -- Bury won it twice and Bolton four times -- to suffer such an ignominy and be the first club to be thrown out of the league since Maidstone United in 1992.
Bury -- who only a few months ago celebrated promotion to the third tier - saw the only live bid to buy the club off Steve Dale taken off the table just over an hour before the deadline.
Dale bought Bury for just £1 last December.
C&N Sporting Risk, a London-based sports analytics company set up by Rory Campbell and ex-Barnet caretaker manager Henry Newman said in a statement they "were unable to proceed" with the bid.
"We are grateful to the EFL for the short extension they granted to us so that we could continue with due diligence, and for their acceptance of our proof of funds capable of mounting a credible takeover," read their statement.
"This has been worked on around the clock by our team and advisors for the past 72 hours."
The company hinted that 'The Shakers' problems ran deep as they said they would be happy to work with the EFL.
"We will be happy to work together with the EFL to share our findings to help them with their ongoing review of football governance," they said.
"It is essential for the long-term future of all members of the EFL and the broader football football family."
Unlike Bury, who had yet to play a match this season due to their financial uncertainty, Bolton had fulfilled most of their fixtures, albeit with a team made up of youngsters.
However, having been close to a deal last Friday the plug was pulled on it reportedly due to former owner Ken Anderson wanting assurances from the administrator Paul Appleton that he would not be subject to repaying any more money once the club ownership changed hands.
Fildraw, the family trust set up by Bolton's great benefactor during their Premier League years, the late Eddie Davies, would not agree to that as it has a charge of £10million for debt.
"Discussions are ongoing with all parties and a further statement will be issued later this evening," read a succinct statement once the 1600GMT deadline on Tuesday passed.
Bolton, relegated from the second tier Championship, were one of the founding members of the Football League in 1888 and were in the Premier League as recently as the 2011/2012 season.
Fans of both clubs gathered at their respective stadia -- Gigg Lane for Bury and University of Bolton.
Bury fans had turned up to prepare the stadium for a match with Doncaster Rovers scheduled for this weekend.
The Bolton faithful collected round the statue of their most celebrated player the late former England striker Nat Lofthouse, known as the 'Lion of Vienna'.
Tuesday would have been his 94th birthday.
Ironically both the historical rivals are due to play each other on Sunday week - a match which is to be televised.