Well, it's not too late to change out the floor if you wanna do that. It will cost you a new drain and enough membrane to do a new floor with enough banding to fold up the walls.
Actually, if you've done a good job of bonding your membrane directly to the top of your existing drain, a case could be made for you to simply cut the membrane around the outside of the drain flange and bond new membrane to the existing on the drain after forming your mortar bed. See my warranty information below.
Another consideration is the thickness of your mortar bed at the drain with this approach. If your drain flange is not sitting above the subfloor an absolute minimum of 3/4" I would not try making a mud bed with the old drain in place.
Entirely up to you whether you want to live with what you've got or spend the extra time and money to have a properly sloped shower floor. I would, of course, vote for the new floor, but the cost on my end will be quite minimal, eh?
[
Edit] Now that I see your last comment, all I can say, again, is that it's entirely up to you. If you fear there might be some pooling of water in the poorly sloped areas, I'd still wanna fix it. But I won't hafta live with it either way.
My opinion; worth price charged.
