Let's try to remove people from the storage system this way.

src/main/java/com/graywolf336/jail/JailIO.java

@@ -352,4 +352,35 @@ public class JailIO {
 				break;
 		}
 	}
+	
+	/**
+	 * Removes the prisoner from the storage system.
+	 * 
+	 * @param j the jail which the prisoner is in.
+	 * @param p the prisoner data
+	 */
+	public void removePrisoner(Jail j, Prisoner p) {
+		this.removePrisoner(j, null, p);
+	}
+	
+	/**
+	 * Removes the prisoner from the storage system.
+	 * 
+	 * @param j the jail which the prisoner is in.
+	 * @param c the cell which the prisoner is in, null if none
+	 * @param p the prisoner data
+	 */
+	public void removePrisoner(Jail j, Cell c, Prisoner p) {
+		switch(storage) {
+			case 1:
+			case 2:
+				break;
+			default:
+				if(c == null)
+					flat.set("jails." + j.getName() + ".prisoners." + p.getName(), null);
+				else
+					flat.set("jails." + j.getName() + "." + c.getName() + ".prisoner", null);
+				break;
+		}
+	}
 }

src/main/java/com/graywolf336/jail/PrisonerManager.java

@@ -336,13 +336,14 @@ public class PrisonerManager {
 				restoreInventory(player, prisoner);
 			}
 			
+			pl.getJailIO().removePrisoner(jail, cell, prisoner);
 			cell.removePrisoner();
 		}else {
 			restoreInventory(player, prisoner);
+			
+			pl.getJailIO().removePrisoner(jail, prisoner);
 			jail.removePrisoner(prisoner);
 		}
-		
-		pl.getJailIO().saveJail(jail);
 	}
 	
 	private void restoreInventory(Player player, Prisoner prisoner) {