This is not trivial and as far as I know this is not supported by Matlab. During the compilation the files are encrytped and a later patching would required to decrypt them. This should not happen on the customer's computer.
So either ship the software in independent packages, such that only the modified functions can be updated, or ship the complete heavy software package for each update.
The virus scanners update their databases only. Updates of the engine work similar to the update mechanism of operating systems: Some libraries are replaced and the list of pointers to the libraries to be used is adjusted.