Obviously hard to say. There have been cases of files being lost or returned (and disappearing into the post of whatever country).
But: IRCC call centre can be inconsistent as well.
My suggestion would be to start putting your 'revised' application together, at least getting organised, putting off the stuff that costs money (translations etc, you won't need to pay the application fees again). Hopefully most of it is just a light revision and you have copies of everything already.
In parallel, try again and again with IRCC. Hopefully they can find your file and determine where it is.