Removing Doubles Destroy Topology Problem:

When two vertices are being too close to each others, during the operation of "Remove Doubles", they merged together as it considered as a single vertex. It happens during my organic modelling, picture below shows before and after removing the doubles from my part of my mesh. Preserving quads topology is the primary, is there a solution to this problem?




Constraint:

This part of the mesh is limited to this size proportion. In other words, it's not rational to just scale up these faces to avoid the problem.

Assumption:

I assumed ensuring no doubles exists is important for avoiding the problem of "Bone Heat Weighting:Failed to find solution for one or more bones." during parenting mesh to rigs with automatic weights.

Solution tried:

Scaling up the mesh by factor of 10 or 20, but it doesn't help in blender to not consider the vertices as doubles.
From what I have seen, you should try adjusting the merge distance. This can be found in the bottom of the tools panel after you remove doubles.



This process will adjust the limit for considering something a "double".