The team is still responsible for the players salary.
You are asking 2 questions though.
1) How does it affect a teams salary cap. This is an OOTP fictional league question because MLB does not have a salary cap. I am pretty sure OOTP includes all salaries, MLB and MiLB to figure the teams payroll.
2) In real MLB the team will be responsible to play the player unless another team claims the player. Then they are on the hook.
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