The answer to the question isn’t quite that straightforward.
In Portfolio 2016, moving files around in the AutoSync folder directly does not preserve the existing records; AutoSync will delete the existing record and catalog the file in the new location. Any metadata that was embedded in the file will be reimported, but custom fields that were not set up to embed metadata will lose that data.
Deleting and recataloging files will cause problems with galleries; Portfolio keeps track of which files are in galleries by their record ID, and deleting and recreating the record changes the IDs of the records, so Portfolio will drop those records out of the galleries.
There are several ways to do what you want to accomplish.
If you want to rearrange files within the watched folder, you can select records in Portfolio Web, right-click, and select “Copy/Move Selection”. Portfolio Web will ask you which watched folder or subfolder you want to move or copy the files to, move the files, and update the records.
You can also move subfolders around in a watched folder in Portfolio Web by selecting the subfolder and dragging it to the subfolder you want to move the files to; Portfolio will move the folder and update the records. Note that Portfolio Web will not allow you to move subfolders between watched folders, as that would cause the records to be deleted and recreated.
If all you need to do is relocate a folder to a new location, you can remove the watched folder entry, move the files to the new location, update the paths so they match that location, then create a new watched folder entry that points to that location.