Delay on end line

[dkmz17]

Last night in Boy's JV game A1 is trying to throw the ball in along the endline after a made bucket, when B1 steps over the line in defending and the referee gives B1 a delay of game warning. He then hands the ball back to A1 to inbound and makes no visible indication whether it is a spot throw in or whether A1 can run the endline. When A1 starts to run the endline, the referee whistles him for a violation and gives the ball to team B.

First, the delay warning doesn't take away A1's right to run the endline, correct?
Second, it is proper mechanics to visibly note a spot throw in or indicate that
A1 can run the endline, correct?