On the right-hand side of any of your scores on Musescore.com, there is a three dotted icon ⋮ Click on it to open all the options and select "Update this score":
- Replace the actual MSCZ file with an updated version.
- Change the score’s "nice link" (e.g., https://musescore.com/yourname/score-title instead of the default https://musescore.com/user/xxxxx/scores/xxxxxx; 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).