R-Group member is not cleaned up after using Clean Up function

**Description:**
The issued was discussed with Alexander Savelyev.

**Steps to reproduce:**
1. Create any structure.
2. Define the structure as R-group member (for example R1).
3. Distort the structure.
4. Click the Clean Up button.

**Actual result:**
R-Group member is not cleaned up.

**Expected result:**
R-Group member is cleaned up.

Reproduce the problem with the listed structure, R-group member, distortion, and Clean Up steps. Trace the Clean Up handling for R-group members and look for existing regression coverage; done means the R-group member is cleaned up and the regression is covered by a test.

Written by the indexing model from the issue text.