I couldn't find a rule or procedure for this, but I think there should be.
At the start of any hand, if a player has a single oversize chip, or two chips of a size that can make the action unclear, the dealer should color it down at the first opportunity - before it's that player's turn to act. At least in poker rooms where the dealers work from track and color up pots during the regular action. I.E. The dealer has the chips to do it without asking a player.
I make this suggestion because I work from a rack in my pub league, and too often I've run into the situation where the player puts his last chip in, and assumes it's all in since it was all his chips - or mumbles something forcing me to ask for clarification.
For example, the blinds are 300/600 and a player has a single 1K chip, or two 500 chips, and nothing else. Breaking down the chips to one 500 and five 100, would make silent action obvious when it's his turn.
Otherwise, asking for a clarification effectively gives the player time to gauge reactions and change their intention.
In this scenario the difference is relatively insignificant. But what if the player was down to a single 5k chip?