Is this a bug?
Yes, track the fix progress at: Custom.css shows empty when edited from within logseq, also randomly un-applies custom.css · Issue #9296 · logseq/logseq · GitHub
Current workaround: Use an external editor to do the job. (The experience is better that way too: you can see real-time changes in pages everytime you save custom.css and you also get more functions from a proper code editor.)