After Kingdom of Flies, more deleted missions of The Phantom Pain were discovered by users who are looking at each game file for more details.
Indeed, the community of Metal Gear Solid V - The Phantom Pain is dedicated to find every trace of things that have been deleted from the game during development, and this time, files related to 8 deleted missions were found by Reddit user TinfoilSnake.
He listed all the game's missions, along with those found. One mission in particular, called Truth: Man Who Sold The the World - the file created by the user, we see that there are more of it - an alternative version of the truth? You also said that missions with the IDs "11041, 11085, 11036, 11091, 11195, 11211, 11200, 11171, 11115 and 11052" are complete in game files were only deleted from history.
When we look at the files we see that the Hellbound missions, Blood Runs Deep, Voices, Skull Face Shining Lights, Even in Death, A Quiet Exit and Truth: The Man Who Sold the World were considered final game, while some missions seem never have been included as history but for presentations, such as E3 2014 and the 2014 TGS.
And no, none of these missions are side-ops, as they have a different identifying the key.
You can check the complete list on the Reddit post regarding this: