You should be able to just change the storage option for your container field to "external" and FileMaker should move the files for you. At least that's how I understand that the process is supposed to work. There's no need to store a self contained copy as far as I know.
Yes, when I did this directly, it only transferred previously embedded images to "external" and skipped the other entries that were previously inserted as "reference only." If there is a way to get the transfer process to perform the same actions on the other images as well, I would also appreciate any pointers to make that happen!
It appears that the external storage solution works for IWP purposes but inserted referenced images do not, which is why I'm attempting this transfer. Our data managers will not have access to the IWP server itself, which is why we're trying to set up external containers so that our database can be accessed by web users as well.
My quickie test shows the same thing, that externally referenced files are skipped during the data transfer to the external location. You may need to use a script to re-insert those files. A script can export them to the temporary items folder and then re-insert them from there.