I don't know the answer to this, it's a legal question in a rather obscure area of the law. (Among other things, it could depend what type of position you held / level - it can be that specific).
Best advice to others who haven't applied yet: DON'T count on time with UN orgs in Canada counting towards physical presence. You'd have been better advised to just wait the extra days before applying but what's done is done.
At this point, if you are still in Canada / accumulating days over the 1095 day minimum, you could/should seriously consider applying anew (withdrawing current). Up to you and your lawyer, if you want their advice - I doubt a lawyer could really tell how long it might take to resolve this.
The issue being, obviously, that even if you 'win' on the merits of your point, it could still take longer to get a decision than a new application.