This could be done by renaming the file directly.
The ipython notebook file will be located in DSS_DIR/config/ipython_notebooks/PROJECT where DSS_DIR is the home of the studio and project is the key of your project (the one you can see in the studio url for example).
Rename it to clean the % sign. For example if you are using linux type in terminal :
mv mypythonnotebookwith_%.ipynb mypythonnotebookwith_percent.ipynb