I was having this SAME issue with the save function on my database. To make things worse my database was MASSIVE and I thought I would have to rebuild it from scratch. Fortunately that was not the case as wix automatically backs up database collections. YOu can easily restore a previous version. See: Restoring a Deleted Content Collection | Help Center | Wix.com
Now for the solution. There is actually two ways to do what you want. If you want to continue using the .save function you will need to pass in all the existing data in the collection field and then just update the value that you want. This can get quite cumbersome and does not account for any future database expansions. So instead I reccomend a wix package called Data helpers.
This package has a function called getAndUpdate that works exactly like you would expect the save function to work. You simply provide a collectionId, an itemId, and then pass a value that you would like to update. You can read all about it here: https://www.wix.com/velo/reference/velo-package-readmes/wix-data-helpers