In AL-only and NL-only leagues players are deleted and salaries refunded when players are traded between leagues. The BBM team that owned the player last will receive a refund of the player's salary. If the salary has been reduced due to an extended time in the free agent pool, the salary when the player was released will be refunded.
If the player is on the 28-man roster when the BBM Commissioner processes the inter-league trade, the entire player's salary (less $100k) is immediately refunded. The remaining $100k is refunded when the player is deleted. This is done to allow managers to bid on possible new free agents involved in inter-league trades.
If the player is in the free agent pool when the processing occurs, the entire salary is refunded when the player is deleted.
Players are usually deleted within 4-7 days from the time the trade occurs. The Transactions page will count down upcoming player deletions.
Note: Players claimed by MLB teams as free agents are not entitled to salary refunds even if they change leagues. Nor are players who retire mid-season. Only traded players get refunds.