I’m not sure, that’s something to try. For a long time we were not uploading folders starting with .. Past threads for reference:
However, I believe at some point (not sure when), we started allowing .well-known folder (at least). I never saw this change being announced (even internally), I just found out about it by inspecting some sites while troubleshooting them.
All this to say, switching to Netlify CLI might or might not solve the issue. However, once you switch, we can at least officially provide support and accept bug reports for unexpected behaviour.