I was a bit surprised that this re-installation did automatically over-write my existing domain-root .htaccess file and showed none of my BPS Free entries in the .htaccess Custom Code boxes, but restoring all of that from my own backup was no problem at all.
Not sure what may have happened on your site, but when you run the Setup Wizard, BPS Pro creates new htaccess files and uses any Custom Code that you have created and saved in BPS free, unless of course you have manually deleted the BPS free Custom Code database options.