@r_demooij
I did a little more research and I think I now have the answer for you.
The MOVE command does not work how you were expecting it. The MOVE command carries all versions, not a specific version. We don't allow moving a document (with all its versions) to a folder that contains a document of the same name, because it could generate a lot of problems with the file versioning.
The good news is that we can use the COPY command to help you achieve your goal here.
Here's how COPY works: as a user, I can copy a specific version of a document from one folder to another so that I can share that specific version with users that should not have access to every version of the document.
For example, an architect will create multiple versions an of a particular document in a "WIP" folder but will want to share specific versions with the client (say, every two weeks) in a "Share" folder. The architect doesn't want the client to see every single version but rather wants to share specific versions for the purpose of meeting contractual obligations or for managing review comments.
If the architect's WIP folder has 10 versions and the architect selects "Copy," the copy of Version 10 will be Version 1 in the "Shared" folder.
After another 12 versions are created in the WIP folder, the architect again selects "Copy" and copies Version 22 to the "Shared" folder. This will become version 2 in the "Shared" folder.
Another example: If the architect's WIP folder has 10 version and the architect selects "copy version" for Version 8, that will be Version 1 in the "Shared" folder.
After another 12 versions are created in the WIP folder, the architect again selections "copy version" (this time for Version 20) in the "Shared" folder. This will become version 2 in the "Shared" folder (edited).
Similar in your case, you can keep uploading all the files to the same main folder and then copy those that you want to the subfolder. After that, I assume you can just delete the duplicates from the main folder.
Hope this was helpful.
If my post helped you, please click on Accept as Solution to validate it so others in the community can find it and benefit from it easily.
Best regards,
Bogdan

Bogdan Ciobanu