Well, obviously if the increase in salaries causes your team to be over the CAP, you'll have to re-do something on your roster. Just because I send out the league numbers doesn't mean you have to immediately enter your team(s).
Last year, the MLB season ended on 10/02 and the new players were released on 10/03. This year, the season ends on 10/01 so the players can presumably be out on 10/02. The next salary increase is scheduled for 10/10. If all teams, including the teams that include 2017 players, are entered and all 16 leagues are ready to go before 10/10, then we shouldn't have to worry about it. Figure the odds of that happening though...