When using Blender 2.79b, BlendMol’s "Remove Doubles" inappropriately removes some faces, leaving holes in the mesh. This does not happen when using older versions of Blender (e.g., 2.79). It is a Blender bug. We have filed a bug report with the Blender team and so expect that future Blender versions will resolve this issue.
Fortunately, most BlendMol users will not need the "Remove Doubles" feature. If you do, please use an older version of Blender. MeshLab can also remove doubles. Exporting from Blender, processing in MeshLab, and reimporting into Blender may be another possible solution.
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