Having same problem. Just updated theme on my site and all my customizations have been wiped out completely: width, colors, tag and category color feature turned off, menu layouts, certain font sizes. No settings will save attempting to fix them. This is a disastrous bug.
ETA: it’s worse than I thought, it’s wiped out the custom CSS I had inserted into the theme via the customizer’s Site-Wide CSS system. That’s a lot of work to have lost. That will teach me not to casually update a theme without backing up my DB. What a disaster.
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This reply was modified 8 years, 2 months ago by jeditricks.