You mean rendering as in green bar over timeline? That is just for previewing.
For export everything needs to be encoded again.
Welcome to the forum.
I have never read of a full-paid version of PrE reverting to "trial." [That has happened with some version of PrPro, but not usually with PrE.]
The Render files are JUST for smoothest playback, so before you go to output via Share/Publish, you can safely Delete the Render Files from the Scratch Disks>Media Cache. There will be nothing lost, with the Deletion of those files, to clear up the watermark, at that time. The files in the Timeline will be Transcoded separately from those Render Files, when you go to output.
The FAQ Entry on working with Projects, that started in the trial, is here: http://forums.adobe.com/message/1966673#1966673
Thank you so much, I managed to figure it out and the watermark is gone again!
Great news, and let's hope that is have been totally banished from the realm!
Thanks for reporting,