The Python Tools Visual Studio seems to cache or generate files, logs and DB in the hidden folder .ptvs
.
Since those data are generated, you should safely ignore that file and never version its content.
See for instance this discussion around the issue "Visual Studio 2010 freezes with PTVS 2.0RC":
Are you using or can you upgrade to our latest dev build and see if the issue goes away?
You may also want to try deleting the (hidden).ptvs
folder in your virtual environment and recreating the DB from scratch.