FTP error 550 (and other 500 errors) are errors reported back from the server indicating an issue connecting to a folder, or modifying/overwriting a file. Unfortunately, because this is a server error where the server is refusing access, it's not possible to fix the error within Freeway. There are, however, steps that can be taken outside of Freeway to allow uploading again.
If the basic FTP troubleshooting steps do not resolve the issue, the best thing to do is create a blank slate for Freeway to upload to. This is done by removing all the existing site files from the server, and uploading fresh from Freeway.
Many hosts can do this for you, so the easiest method is to call your webhost and ask them to reset your site back to default. This will ensure that any files or folders your specific host may require remain on the server are still there. After they've reset your site, you should be able to upload as expected via Freeway. If your host does not offer this service, or if you'd prefer to do so yourself, you can do it manually with a dedicated FTP client. If you do not already have one, Cyberduck is an excellent, free option.
Once you have your FTP client of choice installed, you will first need to connect to the server. In Cyberduck, click the Open Connection button. You will enter the same Upload details that you entered into Freeway to connect to the server in the FTP client. After you are are connected, you will see the files and folders on your site. If you have to put a specific directory into the Directory field in the Upload dialog, you will need to open that same folder before you see your site files.
When you've reached the point where you see your site files, you can select all the files and folders that Freeway uploaded and delete them. Before you delete anything, double check that you've only selected the files and folders that were generated by Freeway; if you select anything that Freeway did not put on the server, those files will NOT be recreated when you reupload the site using Freeway.
Once you've deleted the existing files, you should no longer receive a 550 error when uploading. If you still do, the problem is likely with the root directory, and you will need to contact your host for further assistance.