We've noticed a peculiarity of Copy To vs common File uploads in SharePoint Online. When you upload a new version from non-SharePoint, it adds a new version (replace) and retains the previously set custom metadata, which is fine and as expected. However, when you do the same from a SharePoint location, going to the same library, it replaces the document and versions it, but it blanks all the meta data. This is described in this article (https://andrewwarland.wordpress.com/2021/07/02/metadata-persistence-when-records-are-moved-in-sharep...), but I've not seen much talk about this online within Microsoft communities.
I suspect this is to do with the custom columns being completely different, but has Product group given some thought on what would be most useful for end-users, and whether the standard functionality should version the document upon the user selecting replace, but retain the custom metadata of the version before, as this is quite inconsistent and hampers users using SP, OneDrive, Teams and moving their data around within a business flow.