Ever since upgrading to Xcode 8 using Swift 2.3 I have several missing files warnings. They are all related to pods that I am using.
The files that are missing are
I had this issue on Xcode 9.3
The solution that worked for me: Add a space in the file, save, then wait for the ! status to change to M, and delete the space, save.
Sadly, with nearly a 100 files to go through, I revisited this post, and this comment from @BennyTheNerd to an answer, helped!
For me, it was as easy as quickly disabling and then re-enabling source control under preferences. Xcode > Pref > Source Control > uncheck "enable source control" .... then re-enable it after. And poof! gone! – BennyTheNerd Jan 16 '17 at 7:29
Additionally though, I had quite Xcode and then open the same project, and then re-enable source control through preferences.
Hope this helps!