Hey Chris,
I was wondering if it would be possible if you could post the exact lines of code you changed in your updates? I have modified some of the scripts and would love to be able to just copy and paste your changes manually, instead of through the asset store.
Thanks!
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Edit: An even simpler solution is to store copies of your changed AC files in a different directory. Whenever there is an update, do a full update from the asset store. Then use a file comparison tool to manually merge your changes into the latest AC files.