no, I can't confirm your problem.
To test, I opened the CSS settings for Boost. "Site administration > appearance > theme > Boost > advanced settings > raw scss". I wrote the comment
/* test */ into the first line and saved the settings. Then I immediately restarted the MoodleBox from the MoodleBox dashboard. After this reboot, I was still able to find my pasted comment
/* test */ in the first line of the raw scss.
For the next test I wrote the same comment
/* test2 */ into the first line and saved the settings again. Then I restarted the MoodleBox from the terminal
sudo reboot. Also after this reboot I found the pasted comment in the raw scss.
Best regards, Ralf