Well, it depends on the weight and importance of the modifications.
A typical application may consist of some or all of these items:
- The CVI Rte
- NI-DAQ support
- Some support DLLs
- Your executable
- Some UIR files
- Some support file (configuration files, data files and so on)
Since you are speaking of "minor modifications" I assume that none of the first 3 items is to be modified / updated; on the other hand, since presumably the last item includes files that contain user data it is better not to substitute them with some "default" file.
Given this, your update is likely to include only the executable and some of the UIR files of your application. In this situation I personally tend to send to my customer only the updated files but keep in mind that my applications are almost unique (one application-one customer) and that normally my customers are able / prefere to execute the update manually. In other scenarios, you may want to create a distribution kit with only the updated files not including the RTE and so on.
As a principle, supposing no interaction issue is present (e.g. UIRs with changed panel names, added or removed controls and so on) you may update every individual file without problem.