First, I'm not a pro, nor have huge experience in tiling...whilte tiling over plywood directly with mortar then tile is possible and can last a long time, everything has to be perfect for it to last. Versabond is good for many things, but I'm not sure it is flexible enough to last directly on plywood in your case. When you put the tile back down, make sure you get 100% coverage - if it isn't flat, you may have to back butter the tile to account for the differences. If the lip was caused by there being a gap between the two layers of plywood, the flex when you step on that area will cause continued problems.
If there are any voids or gaps between the two layers of plywood, you can expect problems in the near future. My unprofessional opinion.
Not a pro, multiple Schluter Workshops (Schluterville and 2013 and 2014 at Schluter Headquarters), Mapei Training 2014, Laticrete Workshop 2014, Custom Building Products Workshop 2015, and Longtime Forum Participant.