This was bugging me for a long time now, and I continue to search. It appears that the file is deleted automatically because of a mention of a symlink. So, I opened the file admincontroller.php, search for symlink, then at line 852, I found "isSymlink" => $gpm->grav->isSymlink(). I removed the line, then deleted the comma at the end of the line 851. I re-uploaded the file, and bam, everything (well, except I see 0 plugin and 0 theme when browsing the admin page, but in the backend, they are there and working...) now is working like a charm. I can login again and manage my blog like before.
I got clue from this post on stackoverflow: https://stackoverflow.com/questions/38062279/php-file-getting-deleted-automatically. Since I have CPanel... I decided to try...
For now, this line is removed from the file. Did I broke something? Does this line can be "renamed" in something else, or a fix may be applied. From what I understand, the word "symlink" isn't well received. Maybe it's to avoid a backdoor, or a threat.
Anyway, I just wanted to let you know guys what was the cause of this "mysterious disappearance".