I was thinking they could handle it like historical sandbox games handle historical events where there are a set of triggers that aren't too precise but specific enough that the overall story matches.
Something like
-If MJ wins the title between 92-94 he retires
-When LeBron's rookie deal is up and if he has not won a championship, trigger the decision (even if he ultimately resigns)
-Add some logic that serves to check how many teams have bad contracts or something at the time of a new CBA; if check passes trigger amnesty clauses
These kind of triggers are great for adding some dynamic elements into any franchise mode. They're just if/then statements and can be applied in a lot of different ways. Like all the player personality badges and signing preferences.