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I understand that:

  1. Rigify generates deforming bones on a specific layer, and I can manually adjust (paint) weights after I generate the rig.

  2. I can make change on my metarig and regenerate the rig.

My problem is, do these two features work together? For example if I generate a human rig, manually paint some weights, add a tail on the metarig, and then regenerate the rig, would my manually-painted weights remain untouched?

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Yes, the weights are stored in the vertex groups of the mesh that have the same names as the bones (DEF-spine.006, DEF-hand.R, etc). Regenerating the rig will not touch them.

Just don't use Parent To > With Automatic Weights. This will override your weight painting for sure. You can use Parent To > With Empty Groups (P) to parent the mesh to the rig without changing the weights.

If you separate a part of the mesh, such as the tail, it should be safe to use Parent To > With Automatic Weights for the tail only. After this operation, join the body mesh with the tail mesh again.

You also can make a backup copy of the mesh and restore the saved weights with the Data Transfer modifier if they got messed up for some reason.

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