There is a three-dotted icon ⋮ on the right-hand side of any of your scores on MuseScore.com.
Click on it to check for all available options and select 'Update this score':
replace the actual MSCZ file with an updated version;
change the score’s 'nice link' (only available if you previously set a profile link in your account settings);
change the title of the score page;
change the text of the description that appears below the score;
add/remove tags separated by commas, which appear below the score and help people find related scores;
attach the appropriate license;
make the score private (only you and people you share a 'secret link' with can see it) or public (see Privacy);
delete the score.
As long as you don't delete the score when updating it, any comments, favorites, and statistics will remain.
You can also update the online version of a score directly from within MuseScore, using File / Save Online... The dialog should fill in the existing score information from the website and have a checkbox for 'Update the existing score' (as opposed to leaving it alone and adding a new one).
Keywords: update a score, updating.