I don’t know the exact rules, but you can certainly make some changes. The latest release has more features I have not tried yet around copy / pasting between puppets so you could try creating a new puppet and copy/paste things over to be safe.
otherwise select the scene and duplicate it as a form of backup before you start fiddling.
i have also opened Puppet in CH and AI, made changes, stuffed things up, then undid changes in Ch then Ai then hit the sync button in the scene. I have not lost a project yet that I could not recover... but I still make backups first! just be aware if you change the artwork file and CH forgets details, doing undo in AI is not enough. You need to undo CH to get back to before the last refresh to recover lost rigging
in the rigging window you can type control-E to bring up the editing tool on the right copy of the artwork. Things go wrong the most when you change the layer structure too much. Little changes are generally fine
How I do it is to place the new clothing layer directly below the original and repeat for each layer.
Then create a Trigger or Swap Set to change the clothes either independently or all together.
How that works.
***Hope that works
Thanks for the responses everyone!
What I wound up doing was going into the Puppet panel and changing the puppet file it was pointing to, swapping it for the one modified with the new clothes. That kept the animation we had originally synced to performance.
I should note that we're still on the previous version of CA18, which does not have the ability to copy and paste animations between puppets in a scene (like "Paste Attributes" in Premiere). Hopefully that's in the new version or else a future version.