How to remove local folder from remote project without deleting remote files?
Along the lines of shademan's response, this appears to work, plus is less work:
Mistype your credentials in the project configuration so that the ftp connection will fail. Now, delete all the folders you want from your project. When it tries to delete the files remotely, it will prompt for a correct password. Click cancel! At this point close out of Netbeans and reopen. Then, fix your credentials.
Note: You can click Yes to the "Disable this functionality" message. I was worried it would try again after I reopened Netbeans and fixed my credentials, but it did not.
Also, another solution is to add the folder to your project settings' Ignore list, although the folder is technically not removed.
Hope this helps someone! I agree that there definitely should be a better solution.