I have also had this problem since upgrading to 2.0
I found a fix on the textdrive support site that seems to work – (even though its related to textpattern)
https://kb.textdrive.com/article/webdav-versus-textpattern
change the .htacces to the following
RewriteEngine On
RewriteCond %{REQUEST_FILENAME} -f [OR]
RewriteCond %{REQUEST_FILENAME} -d
RewriteRule ^(.+) – [PT,L]
RewriteCond %{REQUEST_URI} !/(assets|dav|ical|_ical)
RewriteRule ^(.*) index.php
I am hosted on dreamhost and it seemed to fix the problem (but i am still going to move all my webdav folders to a sub domain incase wordpress decides to rewrite the htacess file again)
good luck
Michael