I never had commanders disappear. Maybe it's a consequence of recent website changes, maybe you accidentally pressed "Delete" instead of the "apply changes" button (which btw has a super bad design, can cause confusions and should probably be renamed to a simple text button). Or perhaps module rules were changed and certain configurations were no longer possible. Though I guess that would only result in an empty module slot. Not sure.
Can you explain what happens before commanders disappear? What were your actions? Can you reliably reproduce this problem?
It appears new names for commanders are limited to 20 characters. So to answer your question: Other players haven't renamed their commanders recently.
