Boston must wait to see if they will be accepted back into the Conference after their exit from the Football League.
The Pilgrims were relegated on Saturday after losing 3-1 at Wrexham.
During the game chairman Jim Rodwell entered Boston into a Company Voluntary Arrangement, preferring the docking of 10 points to apply this season.
That has raised serious concerns with Conference bosses, who will discuss Boston's predicament at a board meeting on Thursday.
Conference vice-chairman Charles Clapham said: "It's a unique situation with them going into administration in the last two minutes of the last game of the season.
"Whichever way you look at it, you can't turn around and say that this is sending out the right message in the world of football.
"It might be technically legal, but morally it's sending out the wrong message to creditors.
"In conjunction with the Football League, we'll have to look long and hard at the rules and the legality of it all in order to see what the implications will be.
"Leeds entered administration to save themselves a 10-point deduction next season and now a precedent has been set.
"It seems that clubs are using a loophole in the rules and I'm sure it will catch the attention of the ruling bodies.
"You've got to look at the trail of destruction which has been left behind and the people who've been good enough to give them credit.
"Maybe in the future clubs won't be able to get credit because of this type of action."