W.r.t. facts now explained by the querist in Post no. 2 above, I hold a view that section 50 (3) (& rule 88B (3)) will not apply.
This is because given situation is not that of 'credit being wrongly availed and utilised' but about credit which was due & available to the claimant as the time of availment.
Reversal of ITC / Payment of tax (which is required due to subsequent events i.e. some property could not be sold before obtaining OC (& there is no dispute about Dept's on merits as per querist)) does not make initial availment of ITC as wrong, in my view.
But, if Dept. makes case - against the client - alleging wrong availment of ITC, you can definitely try & use Section 50 (3)r/w 88B (3) to your advantage (besides, checking probability of challenging entire demand on merits, depending upon contents of SCN, nature of allegations, period of dispute and relevant provisions at that time etc).
These are ex facie views of mine and the same should not be construed as professional advice / suggestion.