Lost my saves too. I had my saved games since the release of Mass Effect 3, including all DLCs such as Omega. I wanted to play Citadel today, but got an error message that the saved games are not synchronized or something like this. The date on my local machine was newer than the one on the EA cloud. So I chose my local machine. The game started crashing on start up. After some reading online, I found out that the crash was related to Local_Profile.sav being 0 KB, and mine was. After deleting the file, the game would start normally. But now I lost the last game's profile including the latest saved games.
Also noticed that Origin's support chat wating time is 60+ minutes. I wonder is something went wrong on EA side, and if it's still possible to recover my saved games?
EDIT: I'm not really sure if my problem was related to yours or not, but I solved mine by deleting all the old profiles from Mass Effect 3 dir, leaving only the latest one, by file date. Now I can load it in the game, and got it synced with Origin clound too.