So, this is a bug in Roll20 that I have brought up with the developers DIRECTLY many times. Token IDs (all IDs, really) are Unique across the game. When you drag in a new copy of a token for a creature, it has a new ID. This is absolutely a written rule and the way things always work... ...except that if you transmogrify a map out of the game, rename it, and transmogrify it back, all the tokens retain the same Token ID. This causes the scripts to be unable to identify the correct token, and so anywhere you specify a token id, it will find the earliest instance of that token id and change it. There isn't really a way to get around this other than re dragging in all the tokens again. I might be able to do some hackery with the current page id of the person executing the command to force it to find the ones on the current page, but I'll have to look (Honestly, this comes up so rarely that I haven't had that thought until just now.).