Yes, but the way you go about it depends on which version of the client you are running.
The older clients use Map0.mul, Statics0.mul, and Statidx0.mul for both Felucca and Trammel. The differences between the 2 maps are patched in at run time from other files commonly called the "diff" files, which contain all the differences that are unique to Felucca and Trammel. So to make Trammel a different map than Felucca on these clients, you would need to put all the changes in the "diff" files. There are a few programs that will allow you to do that, TDV Mulpatcher is one of them that will take 2 maps and then create "diff" files for the differences between them. I've tested this and you can actually patch an entire full map that is completely different using "diff" files.
For the newer clients (I think clients past version 6.0.0) its a little easier. They put Trammel into its own map in the newer clients. So now Felucca is in Map0.mul, Statics0.mul, and Staidx0.mul; while Trammel is in Map1.mul, Statics1.mul. Staidx1.mul. So for the newer clients its just a matter of editing the appropriate map.
Hope this info helps!
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