there are some simple fules to follow when merging a flipped geometry.
first of all -> make the faceNormals show up. then you will understand better what I am talking about.
if you flip (scale in a minus direction like from X to -X) you can run into some problems afterwards. my workflow is this:
flip geometry. then do a freezeTransformation on the flipped geometry. as you can see, the normals flipped also now pointing to the inside of your geometry. this is bad. you can merge vertices from 2 objects which have diverging faceNormals but you create a nonmanifold geometry by doing so. to avoid that you freeze transformation and reverse normals. now all normals point into the same direction. when applying mergeVertex now the seam between both objects should dissappear.
if not all of your verts are merged they probably have different distance to the flipping axis. to bring all in one line quickly activate the move tool. in the tool options uncheck Retain Component Spacing (dont forget to check it again after). this makes sure the selected verts dont have a single pivotpoint. if you use the X-key now on your keyboard while moving, the selection gets snapped to the grid. since you turned off ret comp spacing all verts snap to the grid and not just the selection´s pivotPoint.
and don´t ever use instance duplication if you want to combine things! this would be bad also! XD
sorry for my bad english! hope you understood what I tried to explain.
everything starts and ends in the right place at the right time.