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The WP_Theme object is very different now. I've added a version check to maintain backwards compatibility. Eventually the whole transient_update_themes_filter function should be refactored.
Fixed in v1.3.6. Deployed to WordPress Plugin site.
Excellent work, Chris! The new version v1.3.7 works very well and I've been able to both roll back and automatically update sites with no issue. MANY thanks for fixing it.