PSI Thanks for the response =) That makes sense, I had a vague idea that I was going to need to update all my events after importing with the new Spriter format so it's good to have confirmation on that.
I did some more testing and it seems that my simpler legacy animations work fine when resaved as .scml and .scon with the proper custom save options, so that's a relief. Unfortunately my main character which by far has the most animation data still has the invisible sprites/animation problem.
Also, when I try to play an animation with a "Set Animation" event it pops up the following error:
Uncaught TypeError: Cannot read property 'length' of undefined
http://localhost:50000/Spriter_plugin.js, line 2272 (col 32)
Okay, just tried deleting all but one animation in the file and it worked, so maybe I'll just have to go through 38 animations and find out which are causing a problem.
Found the culprit! I had saved a new version of this character's head sprite into its root folder and made the mistake of swapping it in C2 rather than overwriting it. When my animator went to work on it in Spriter, she swapped in the alt sprite that should have just replaced the old one. To fix the duplicate sprite I had edited the scml file manually to remove any reference to it, which worked fine except for this one animation. On a few frames, the object list showed a blank sprite in the Z-Order list and the head was remaining in place while the bone moved, so I swapped it for the sprite it should be and all is working properly.
In the future I will definitely avoid adding unnecessary and confusing pngs to the root of the animation folder.
Now to resave all the other animations and fix the event references and move the updated names into their appropriate folders for organization and make sure the new sprites are in the right families.