Hi,
I do quite a bit of this sort of thing using JSON files in certain situations where a Database is not practical. The way I go about it is to Serialise and Deserialise the files into class objects that can then be used in the project. By doing things this way you could, for example, release a project with a file that has 5 Properties and your users begin to use that file. You then release an update to your project with 6 Properties in the file now. The Next Time the OLD file is read only the 5 Original Properties are read into the Class Object but the Next Time the File is written it then writes it with the 6 Properties ready for reading again later.
All this will depend on exactly what it is you are doing but hopefully this should give you some idea about where to start.
Hope that helps.
Cheers,
Ian