The development process of scientific applications is largely dependent on scientific progress and the experimental research results. Thus, dealing with frequent changes is one of the main problems faced by the developers of scientific software. Taking into account the results of the survey conducted among scientists in the HP-SEE project, the implementation of change management and version control software processes is inevitable. In this paper, we propose software engineering principles that should be included in the development process to improve the version control and change management. Moreover, we give some specific recommendations for their implementation, thereby making a slight modification of already generally accepted templates and methods. The development steps practiced by scientists should not be replaced completely, but they need to be supplemented with appropriate practices, documents and formal methods. We also emphasize the reasons for the inclusion of these two processes and the consequences that may arise as a result of their non-application.