Ok, First: TWO switches control the outside lights? That is different (unless one controls a light on one side and the other the other side, or a normal patio light and some big "Scare" lights)
Second: The third switch... I do not know how it can turn them off and you can still turn them back on less all the lights are either "Remote" (Never heard of that) or 3-way (Likewise) and if that were the case (3-way) Flipping that door switch would change the status of all lights.
That switch on my rig only controls 3 out of six lights by the way.
I suspect it is the battery disconnect and that is why when you re-connect if the batteires are very hungry they pop the fuse on the converter.
Home is where I park it!