Cecchi,
Beekit does not import or export code changes, but only changes in properties (header files)
you should use the Export properties feature as it does not overwrite any source code file (except for the endpointconfig.c).
Export solution will give you a new copy of all source code, export properties will not.
Note that changing the ZTC enable/disable function does require you to re-import the project file.
BR,
Mads