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Like many CATIA messages, this one doesn't seem to make much sense to me either.
I was able to recreate your steps, and I also got the same message. But when I clicked the OK button, a new untrimmed surface was created based on the Bounding Box, as the warning message said. But not the original Fill surface (as I expected). I did get better results with I used a Extrude surface instead of a Fill surface.
I guess that message is just a warning that the new, untrimmed surface will not match the surface you started with.
I didn't see anything in the online Help explaining this.
I have never used the Untrim tool, and I'm curious why it exisists. Since CATIA V5 is history-based, the original surface is still available even after it has been trimmed.