Does FNVEdit show any conflicts on the locations? I use a ton of FO3 location conversions, and they've all worked fine.
And regarding the above post, if GECK is bombing on syntax errors re: the Label lines, you don't have NVSE properly installed to work as a plugin for GECK. Label is an FOSE/NVSE command. If you manage to get past the Label lines, it'll bomb on the ListGetCount and ListRemove commands as well.
Per the source itself:
"Scripts written with these new commands must be created via the G.E.C.K. after it is launched via nvse_loader. Open a command prompt window, navigate to your NV install direcory, and type "nvse_loader -editor". Alternately you can create a shortcut to nvse_loader.exe, open the properties window and add "-editor" to the Target field. The normal editor can open plugins with these extended scripts, but it cannot recompile them and will give errors if you try."
Check, double check, triple check.