Hearts and Partick Thistle could face expulsion from the SPFL after the SFA hit them with a notice of complaint following their legal battle.
Both clubs have been charged with breaching SFA's rule 78 after their efforts to avoid relegation via the court of session and will now face a compliance hearing on August 6.
The rule states: "No member or Associated Person shall take a dispute which is referable to arbitration in terms of Article 99 to a court of law except as expressly permitted by the terms of Article 99."
Under normal circumstances, if the rule is breached, clubs can be kicked out of the SPFL and have their SFA membership revoked.
But Lord Clarke flagged up the possiblity of the SFA going down this route in court and he believes it could be viewed as unlawful for Hearts or Partick to be booted out of Scottish football under this ruling.
He said: "In my view, a further issue arises from a point made by Mr Moynihan QC on behalf of the SPFL about the disciplinary process and the potential sanctions applicable to SFA members. I was taken to the SFA’s Judicial Panel Protocol and shown a provision which applies where a member or an associated person takes a dispute, which is referable to arbitration in terms of Article 99, to a court of law, in circumstances other than those expressly provided by the terms of Article 99.
"The provision refers to penalties of up to £1,000,000 and/or suspension or termination of the club’s membership of the SFA being imposed if a court action is raised. In my opinion, the existence of that potential penalty (which includes expulsion or as Mr Moynihan put it, being put “out of the game”) is a factor which requires to be considered when analysing the lawfulness or otherwise of Article 99.15
"In response to a question from the court, Mr Borland QC, on behalf of Dundee United, Raith Rovers and Cove Rangers, accepted that this matter should form part of the context in which the lawfulness or otherwise of the terms of Article 99.15 fall to be assessed."
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Hearts and Partick were furious with the SFA's "oppressive" charge.
A joint statement read: "We are incredulous to have received a Notice of Complaint from the SFA in the circumstances.
"It is oppressive of them to require submissions from both clubs by 20 July when we are, in terms of their own articles of association, actively engaged in arbitration.
"As our focus must be squarely on that, we have already requested the SFA to review the timing to allow us to be properly prepared and represented. That is the very least we should expect from the process."
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