Spot on. There was another element to the 2014 stitch up as
@Prestwich_Blue has elaborated on in the past.
Pre-2010 contracts were originally not considered part of the expenditure calculations as even UEFA deemed it unfair that clubs could be punished for expenditure contracted before FFP even existed. This was according to Annex XI of the FFP rules.
City asked UEFA 3 times if they were on track with their accounts and 3 times UEFA confirmed they were. City duly submitted their accounts and UEFA promptly changed the 'toolkit' (the method of calculating Annex XI exemptions) which dropped City in the shit. PB has pointed out that City would have failed FFP anyway but within mitigation limits. After UEFA's dirty trick City had suddenly failed FFP by a much bigger margin.
The subsequent 49 million Euros fine, two thirds of which was refunded as you correctly say, resulted in Khaldoon reluctantly left to 'take the pinch' but only on the basis of drawing a line under the matter for good. That's why when the last UEFA stitch up happened City refused Ceferin's offer of a limited punishment because it implied acceptance of guilt when City had done nothing wrong. City appealed to CAS and were exonerated of any financial wrongdoing leaving UEFA looking like the vindictive shower of shit they are.
On a side note Liverpool DID fail FFP in 2013 but got away with it because they failed to qualify for Europe that season so fell outside UEFA's remit for investigation and punishment and there was no Premier League version of FFP at that time.