I'm Doug, and I'm sorry to hear of the confusion. My goal is to provide you with excellent service today.
I'm sorry to have to say that covenants like the one you described---a Restrictive Covenant--- always run with the land and regardless of how many times the property may change hands, and whether or not the covenant language is left out of a later deed transferring title, the covenants are enforceable and bind all owners of the property.
If the area has been rezoned to a multi-family zone, while yes, the new zoning law is in conflict with your particular lot---the covenant may still be enforced through the court system.
There is a way to avoid the covenant however it may be difficult if you cannot get the cooperation of your neighbors who may benefit from the covenant. If you file an application for a planning permit to remove or obtain a variance of the restrictive covenant, notice of the application must be given to owners and occupiers of land in your geographical area who are being arguably benefited by the covenant. Also, usually you must post a notice of your application to remove the covenant on your property and post a similar notice in the paper.
While this can be an effective way to get around the covenant, I would strongly urge that you retain a local real estate law attorney to assist you in getting through the legal hoops. In the end, if your neighbors don't object, then it is possible to have the covenant removed.
You may reply back to me using the Reply link and I will be happy to continue to assist you until I am able to address your concerns, to your satisfaction.
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I wish you and yours the best in 2015,