Unexpected holes after Remove doubles

Hi. Can’t check the file but you most likely offset the other side for a distance that was too small.
When you use Remove doubles, it merges all vertices that are within 0,0001 radius from each other.
If this is also the distance you choose when adding the other side, then naturally Remove doubles merge them together.
The most reasonable solution is to undo the action, select the whole mesh, deselect the areas where you added the other side, then remove doubles.
But if you can no longer undo it, just increase the Merge distance until all other side disappears completely, recalculate normals and add a new other side