The Curious Case of the Disqualification

Context

Mr. Faizal was convicted by the Kavaratti sessions court for attempted murder, and sentenced to 10 years imprisonment.
Later on, the Lok Sabha announced that he was disqualified as an MP with effect from the date of conviction.
The Election Commission of India (ECI) fixed the date for by-election to that constituency. Mr. Faizal appealed to the Kerala High Court for a stay on his conviction and sentence, which the High Court suspended.
The High Court said that the consequence of not suspending the conviction is drastic not just for Mr. Faizal but also for the nation. The cost of a parliamentary election would have to be borne by the nation and developmental activities in Lakshadweep will also stop for a few weeks.
The elected candidate will have just 15 months to function till the end of the term of the current Lok Sabha.
Given these exceptional and irreversible consequences, it suspended his conviction until disposal of the appeal.

The specific provisions:

The provision for disqualification is given in Article 102 of the Constitution. It specifies that a person shall be disqualified for contesting elections and being a Member of Parliament under certain conditions. These include holding an office of profit, being of unsound mind or insolvent, or not being a citizen of India.
It also authorizes Parliament to make law determining conditions of disqualifications. There are analogous provisions for members of state legislatures.
The Representation of the People Act, 1951 provides that a person will be disqualified if convicted and sentenced to imprisonment for two years or more. The person is disqualified for the period of imprisonment and a further six years.
There is an exception for sitting members; they have been provided a period of three months from the date of conviction to appeal; the disqualification will not be applicable until the appeal is decided.

Differential treatment:

The differential treatment of candidates for elections and sitting members was challenged under Article 14 (right to equality). A Constitution Bench of the Supreme Court, in 2005 (K. Prabhakaran vs P. Jayarajan), decided that the consequences of disqualifying a contestant and a sitting member were different.
In the latter case, the strength of the party in the legislature would change, and could have an adverse impact if a government had a thin majority. It would also trigger a by-election. Therefore, it was reasonable to treat the two categories differently.
The Court also considered whether in case of a disqualified candidate who is later acquitted, the disqualification would be removed with retrospective effect.
It stated that this could not be done as this would require the results of the election to be canceled. Therefore, the removal of disqualification would be prospective and for future elections.

Lily Thomas case:

This issue was also discussed in the Lily Thomas judgment (2013). The judgment stated that a disqualified person may obtain a stay on his conviction, and cited an earlier 2007 judgment that the disqualification would be removed from the date of the stay order.

The Legal confusion:

The Lakshadweep seat was declared vacant but the ECI, after the stay order, announced deferring the by-election. The Lok Sabha has kept the seat vacant and has not yet reinstated the MP. The reason the High Court granted the stay was to avoid an expensive election.
The question is whether the removal of disqualification can be back dated as if it never happened and the election avoided. Or whether the disqualification is removed only from the date of the stay order, and, therefore, the vacated seat be filled only through a by-election.
This conundrum arises because the Lily Thomas judgment requires the seat to be vacated immediately upon disqualification whereas the Kerala High Court stay tries to ensure that the MP retains the seat until the appeal is decided.
The answer will also have implications for similar cases in the future.