Has the conversion done something to security? Depending on the server settings, the files may only be listed if the user has access to them, so that may be one to check.
It sounds like you went into the Database area of the server via the OS interface to place the files instead of using the Server Admin tool to upload the files to the proper location. Because you didn't have the Admin Tool handle this, you will need to go in and set the permissions on the files at the OS level so that FM Server has read/write permissions to the files. The Admin Tool set these permissions during upload, but they do have to be set.
Also check the Server Admin tool to see if the databases are even open on the server, as it may not have proper permissions to even server them.