The League is also concerned that there is "little prospect" of football creditors being paid in full under the CVA - which is a requirement of the League's articles and insolvency policy.
Proposed modifications put forward by the League to resolve the issue were rejected - at "great concern" to the League.
The timing of any 10-point deduction (called "sporting sanctions" by the League) would be crucial to the survival hopes of both Boston and Wrexham.
Reports have claimed that if Boston were losing and looking set to be relegated to the Conference anyway, they could attempt to enter the CVA during the game - and suffer the 10-point deduction immediately which would have little effect in real terms.
However, if they beat Wrexham and stay up, they could delay the CVA until after the season is over in order to take the 10-point deduction next season in League Two.
Ironically, Wrexham were the first Football League side to be deducted 10 points for entering administration, during the 2004/05 season, which saw them relegated from League One to League Two.
However, in 2006, Rotherham were in danger of relegation from League One going into their final game of the season, which was also a winner-takes-all game.
Having drawn 0-0 with Milton Keynes to ensure the Dons went down instead of them, Rotherham then entered a CVA in the summer and were deducted 10 points at the beginning of this season.
But on Friday, Leeds United - all but relegated from the Championship - went into administration with their 10-point deduction imposed immediately, allowing them to start next season in League One on zero points.