The Scottish FA are still to sign off on a rule change which allowed the Old Firm to insert B teams into the fifth tier after it was voted through by the clubs.
And clubs believe there is a possibility this approval will not go through unless teams in the Lowland League vote to scrap the boundary rule which decides where relegated teams from the SPFL will play.
At present, whether a club plays in the Highland or Lowland League is decided by their location in relation to the River Tay.
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Angus side Brechin City requested to play in the Lowland League following their relegation at the end of last season but, despite warning from Hampden chiefs about potential repercussions, clubs voted against it unanimously.
A row has now broken out regarding information being passed to clubs on whether there is a potential threat to the colts or the ability of the Lowland League to nominate its own team to the SPFL pyramid play-offs.
Civil Service Strollers vice-president Thomas Brown has stepped down from the league board over the issue.
He told the Daily Mail: “I feel strongly that the Lowland League clubs should have been given all the information available to them ahead of the Special General Meeting next week.
“As the board voted against this I feel this leaves a question mark over the integrity of the board's decision.
“As a result I had no other option than to stand down with immediate effect.”
The Mail reports others could follow.
Another potential ramification surrounds invites for Lowland League clubs to participate in both the Premier Sports Cup and the Challenge Cup, this season renamed the SPFL Trust Trophy.
Celtic and Rangers saw their colt teams voted into the league in the summer on an initial one-season basis.
Rangers colts have started the season in fine form, winning six of their seven league games and sitting just a point off the top of the table with a game in hand. Celtic sit in seventh, winning four, drawing two and losing one of their matches thus far.