If I understand, you are making changes to the artwork file but they are not getting loaded in CH automatically any more? If I understood, some things to check.
If you click on a puppet, at the top of the properties should be the path name to the puppet artwork. Make sure this file name is the same as the illustrator file you are editing. Sometimes CH sucks a copy of the artwork into the project, so you can end up with different files.
If you type CTRL-E in the rigging window, it will start up Illustrator etc on the file CH is using - using the above path.
Another thing is there is a checkbox near the path name field, asking CH to autorefresh on file change. Make sure this checkbox is selected. Maybe turn it off then on again.
In the scene window, there is also a refresh button. To arrows in a circle. Try clicking this button. Then if it does not work, try clicking while holding down SHIFT (I think). Then try restarting CH while holding down the SHIFT key. This is different levels of cache flush, forcing it to reload stuff.
Also note you can redo things in the history. But when you undo “import file changes” things can be a bit funny (where the scene “refresh” can help).