He's not out till you call him out.
A safe call is almost unimportant. The times when I feel it is important to make an emphatic safe call (and the others are unimportant) are a tight play at 1st, a missed tag, a missed catch, a close pick-off play, or a missed base by the defense (like the front end of a double play).
In the scenario you posed, I would not make any call. PERIOD. Until it was determined that he was out or he was safe. When he is off the base the runner is in jeopardy AND THE PLAY IS NOT OVER. Make no call until it is over.
The 3rd baseman may not realize that he is off the base and may come up throwing to 1st.... now you need to direct your attention to 1st. Anything else may mean that you have entered the game by tipping off the 3rd baseman that he should be trying to tag the runner.
The safe call only needs to be made when an attempt to put the runner out is being made by the defense. Otherwise the action can nearly be ignored (A simple safe signal and a quiet to moderate volume call can be made as the game situation dictates.) If the play is important to the immediate defensive action, a stronger, louder, more emphatic signal and call needs to be made.
In your situation, I suggest that you wait and make no call unless the defense attempts a tag. If no other play is being made and the runner scrambles back to the bag, then a simple safe signal is adequate.
