This seems to me no different from other web forms - as far as I know, most web forms that allow for uploading let users keep re-uploading a file. It only makes sense - if a user changes their mind and wants to upload a different file, they should be allowed to.

That sounds reasonable, but in those web forms (email, forum attachments, even on bugzilla here), no file is actually uploaded until the form is submitted. Since that process is actually completed, it makes sense to disable further uploads to cause the user to look to the next steps in the process of completing the Semantic Form.

One issue that arises is when images are uploaded but no semantic data is applied to them, is they can be "lost" if they're supposed to be semantically organized and findable.

Allowing the user to upload a different file is not prevented. They just need to click whatever link brought them to the Semantic Form again. Of course there are other ways too, namely the ordinary MediaWiki upload system. Off the top of my head, I can't think of a situation where an SF single-field upload system would be preferable for repeated use than either the plain upload system, or one of the multi-upload extensions.

What do you think?

It's preferable for the situation where a user uploads a file for a field, changes their mind and decides to upload a different file.

There are other situations that require other preferences, as I have described.

And, even in your preferred use case, the user wouldn't be uploading a DIFFERENT file, they would be uploading an ADDITIONAL file. The way the upload form field functions now is misleading, and flawed for any use case that requires semantic data to be applied to the file. Your preferable way of functioning is encouraging that problem.

Setting to "wontfix" - if users want to upload another file, and replace one file with another in a page, they should be allowed to.