During the API generation step of CyDsFit the .cyfit file gets generated. It is an internal database for PSoC Creator to hold data on the results of the code generation. It is regenerated each time the project is built and a timestamp gets attached to it which might be why you are seeing some changes. Creator uses this file to identify project variation during build without w/o having to re-run previous phases (assuming that the results from earlier phases are available on disk).
Please refer this KBA to find out what to include for version control: Revision Control for PSoC® Creator™ Projects - KBA86358