Hi @John Wilson
So I think the issue is that you plugin is running first BEFORE the real ACF plugin.
What you need to do is hook into the plugins_loaded action, and there you can include your ACF plugin. This will make sure any real ACF plugins are already initiated.
I will do some work to make sure these issues do not happen in the future with better validation in the core for duplicate files.
For now, however, this is your best bet.
Cheers
E
