Interesting question BJ. Here's how I would react in this circumstance:
1) The BB doesn't have anything to "call", he's already in for the full BB of $400. The single overchip rule being just a call IMO applies to anyone who who is responding to a bet in progress... the BB isn't responding to a bet in this case.
2) By "switching" from $400 to $1000 the player has increased the amount of $$ in front of him when facing the option to check or raise...
3) The action is completely unnecessary if he's only wanting to call as he already has the $400 "call" in front of him.
4) But there's another issue... if it's checked to you (that is there is no bet you have to call), and you toss out a single chip, it's a bet up to the maximum allowable of the chip (TDA Rule 32, last sentence). That condition is more similar to this situation IMO as the BB was not facing a bet at the time he increased the total in front of him to a single $1000 chip.
Based on the above, I would tend to consider this a raise to a total of $1000, i.e. $600 raise to everyone who has called the BB. Another thing to consider is that the player hasn't declared anything verbally one way or the other so in the absence of a definitive rule the interpretation goes to how the TD sees it at the time and.... "it's the players responsibility to make their actions clear... (TDA Rule)". So, if they intended a call they didn't make it very clear, if they intended a raise they didn't make that very clear either... it's up to the TD to make the call based on all the facts at hand in this case, and if it's a ruling other than what the player intended, they'll be more careful next time... it's the players responsibility to make his actions clear, not the TD's responsibility to be a mind reader! Lastly, there's also the issue of maintaining discipline in the betting process. I don't like it when a player reaches out and pulls back chips they've previously bet if the action isn't 100% clear as to why they're doing it. By ruling this a raise you serve notice that you take casual "chip shuffling" seriously... Thanks for the very interesting question. (PS: Welcome aboard, glad to see you navigated the registration system).