Undo of clear canvas operation causes molecules bonds overlap atom labels

[AlexeyGirin]

Steps to Reproduce

1. Go to Macromolecules - Flex mode
2. Load from following MOL v3000 from clipboard:

  -INDIGO-02192518422D

  6  6  0  0  0  0  0  0  0  0999 V2000
   15.8598   -8.2251    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   17.5902   -8.2246    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   16.7266   -7.7250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   17.5902   -9.2255    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   15.8598   -9.2300    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   16.7288   -9.7250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  2  0  0  0  0
  1  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  4  1  0  0  0  0
  4  2  2  0  0  0  0
  2  3  1  0  0  0  0
M  END

3. Press Clear canvas button
4. Press Undo button

Actual behavior
Bonds overlaps labels

Expected behavior
No bond overlaping

Versions

• Ketcher Version 3.1.0-rc.3 Build at 2025-02-11; 20:29:49
• Indigo Version 1.29.0-rc.1.0-g2e30df8f7-wasm32-wasm-clang-19.0.0
• Chrome Version 133.0.6943.54 (Official Build) (64-bit)
• Win10

Issue found while testing: #5359