When using the RANK() OVER (PARTITION BY ...) construction in Teiid Designer, the RANK() is always deleted when saving the transformation query (between source and view) in the transformation editor. If you want to use this construction, you have to put RANK() manually into the *.xmi file.
That means that Designer has not added for that language construct yet, you can open up a enhancement JIRA for it. BTW, manually editing the .xmi file and adding it there is of no use when you deploy the VDB in server, as Teiid server does not look at XMI files for metadata. For interim you can use Dynamic VDBs with DDL if you want.