if anyone interested, I came the solution to copy the whole document (.psx and .files) before opening the new created document.
if os.path.isfile(project_path) : os.remove(project_path)
if os.path.isdir(project_path.replace('.psx','.files')): shutil.rmtree(project_path.replace('.psx','.files'))
shutil.copy(init_project_path,project_path)
shutil.copytree(init_project_path.replace('.psx','.files'),project_path.replace('.psx','.files'))
os.remove(project_path.replace('.psx','.files')+'/lock')
#start photoscan
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doc = PhotoScan.Document()
doc.open(project_path)
chunk = doc.chunk
doc.save()