I have many and many websites to manage...so It's impossible & crazy to do that manually on each website.
Hi Laurent.
It looks like a workaround for this does not exist. The template update drops everything that is in template.css & default.css to default values if Compile SCSS to CSS is OFF.
Of course, the Joomshaper team needs to think over this behavior and correct it. But I'm afraid you have to wait until the next update if they take it into work.
Personally, I never come across this problem, because I prefer CSS coding instead of the template settings. I have long understood that the template settings are unreliable when updating.