Design happens all the time, not least of all during the development phase of a project. The work that is done before that should establish a good base to proceed from but never be expected to be a complete and perfect design bible. It is rather a living document that needs to be adjusted and supplemented as need arises (such as technical requirements or altered client needs).
Please note! This is why it’s so important to not do too much detail work in the design phase. Establish a base, structure and principles. But also make sure to be present through out the development phase and tweak things as needed. The stronger and more concentrated (non specific) your design system is able to be, the easier it is to adapt things when the requirements have changed.
In order to make sure that the original design idea is followed it is important for you, its author, to think long term. Document your choices and underlying thoughts well and easily accessible. Preferably directly in Spacecraft. Try to author your design system in such a way that it establishes a base for long term development. Rather than designing every little component/view in deatil, create a base structure, esatblish principles, well thought out typography and so on. Things that can be applied and built upon during future development.