Hi Jacqueline and Jeremy,
Thank you both for reporting this. I was able to reproduce this obscure issue and identify the cause.
The theme settings page was processing form data unconditionally on every request, including empty or incomplete ones. When that happened, all checkbox-based settings (custom theme toggle, scroll-to-top, consent message, custom CSS, etc.) were being blanked out and saved over your actual configuration. This could be triggered by things like a server’s post_max_size being exceeded, a truncated request from a slow connection, or even a browser glitch, which explains why it seemed random and was so hard to pin down.
Apologies for the frustration this has caused. A fix will be included in the next release.