For exactly this reason I use CamelCase or sulkingCamelCase in the names of my functions. Then future additions of built-in toolbox functions will not invalidate my code, because (only most!) Matlab functions use lowercase.
I let FEX: UniqueFuncNames check the uniqueness of names during the installation of my own toolboxes to control this problem.
If the collision appears already, it is the best idea to rename your function and change it in all your source code files. There are some functions in the FEX which assist you in finding the occurrences. This is another good reason to avoid eval in general, which could hide the function names too easily.