Are we talking a workflow in general or a specific project?
It isn't losing links to rendered files. I played back some renders in VLC and there was no WARP on them. The rest of my effects were rendered.
I started running some tests. What I found is that the Warp Filters work on rendered frame information from either the original data or the rendered data. The indicator in the window just lets you know that the information you are being shown has an unrendered effect. Warps render on the fly, by affecting the render info using your cache locations, not the effect render locations. I noticed in a system profiler app that the warps, when on, cached to a disk more often, and that memory was utilized almost twice as much. When altering the warp settings, the caching was instantly running, and ram as well.
The logic for that seems simple enough. The data manipulation for any section of a warp filter beyond the background detection requires the original frame information as well as the adjusters from the other sections (Implicitly defined adjustments that probably use some if\else branching to alter the adjustment patterns). However, Warps appear to be INPUT ONLY actions. They only render in a complete output, not an effect render.
One set of tests I ran was particularly interesting, and it gave me more than a few ideas that might help.
Try nesting your clips in sequences of their own, add all your effects, then place those sequences where you want to place your clips. Render the nested clip. It won't change even if you adjust the warp on you master clip. The reason is that the warp works from your caching, and the nested sequence from the renders that are based on the source sequence output. It will show as unrendered, but it will still have the location of your last render, and will utilize the most recent render. When you render the effects again, the warp will be reapplied and the new render will be used. I would also point out that the old ones aren't always deleted, so, you'll want to adjust your warps as few times as possible.
Note that it will have the unrendered color bar, but it will function rendered.
Another way to handle warps is to handle them in a nested style if you handle them first, like above, and then place all your other adjustments on top of the sequence-clip (using the sequence as a clip), which should render out (even if it doesn't show fully), and only render after you are satisfied with the warp. Then you can apply other effects and have them render nicely. It will still show as unrendered (the warp is running from cacheing, and is being evaluated when you open premiere, but your renders should still playback just fine. However, I did see some stuttering when I used higher grade footage.
With h.264 at 10-15mb\s proxy, it works fine. Higher than that, and things begin stuttering. The Profiler I used showed graphics memory was a bit strained, and the access to the disk I used for renders and footage were lagging a bit, when using a nested clip. Use fast disks and separate them if you can. Put your renders on something fast, and keep your starting footage on something fast. By separating things a bit, you multiply the speeds at which you can access the data. I split up everything to some SSD's and was able to do better with 25-40mb\s proxies (this is a fair balance between quality and speed for me; when I actually do my final output drop, I use DNxHD at high quality with huge files to start, and drop it down to h.264 at 10-15mb\s for a faster playback, small filesize, and faster upload).
It would seem to me that the warp effects are primarily running from memory or caching. This would be a strategy for increasing the speed of the effect upon adding it, but slow due to it's re-applicative nature. This would hint that the effect itself is still under some redesign, opting for wetting the appetites of users and determining it's marketability. I don't know where to give feedback on this particular set of effects, but if you find out, please post it. I'd like to send my complements on the usefulness of the effects, but add that I desire more from their overall functionality.
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