According to the IPL replacement rules, an injured player can be replaced only by a player whose base price in the auction is less than the price the injured player was bought for.
For eg: Consider the case of Mitchell Santner who was signed up by CSK, but is ruled of out of the IPL owing to an injury.Not sure about the exact amount but I guess he was bought for some 75 lakhs.Now CSK can replace him only with someone whose base price was less than 75lakh in the auction, the can't replace him with a Joe Root(Base price-2 lakh).
Yes, injured players will automatically be drafted into the squad the next season unless the franchise lets them go!.