I had a the same problem going from 3.5 to 3.6.4. If I remember correctly I lost the admin user with the upgrade to 3.5.2. One method I have sen recently to correct this is create a new user with publish (or whatever you password is). Dig into the database and manually create one their using that encrypted password. The 'Admin' user is user 14. Also be sure to create a entry in ezuser_setting to show user 14 as enabled ('1').
BTW, I also lost my anonymous user and <b>all</b> of my links.
Like I said< Ibelieve I lost them in the upgrade from 3.5.0 to 3.5.2, a necessary step according to the 3.6.0 docs. What was unclear was which upgrade scripts were required to be run. I ran them all and Lost all URLs and admin and anonymous user. No other users were lost as far as I can tell.