There are 2 types of nets, perch nets are on the bottom and I am guessing less than 10 feet high, you can troll over these as long as you are sure all your gear is a lot further than 10 feet from the bottom, these nets are marked at each end with a flag, they are required to identify the nets owner so a number or name or some identifier will be on the flags. These nets often run for a long ways so you may not be able to see both ends. They normally run these north and south.
The other type of net used is a can net, so named as it is held off the bottom by bottles or cans. This is used primarily for walleye. It can be at any depth , but it is ok to run , not troll between the bottles. The gates Horty is talking about is where there 2 flags within a hundred yards of another. I believe his advice is good that you can troll between, I personally do not. My advice is to avoid nets and give them at least a few hundred yards. As far as getting your gear back if you get into a net, I have never heard of that happening.