The layout changes when opening saved KET/Molfiles formats using the CHEM object.

[NadezhdaPeskun]

Steps to Reproduce

1. Micro mode
2. Load from KET file: CHEM Objectsss.zip

3. Select and Remove several structures (3 Structures are stayed)

4, Save as KET file again
5, Save as Molfile V2000 file
6, Save as Molfile V3000 file
7. Open these file again.

Actual behavior
a) Layout is changed while open Saved KET file ketcher (3 chem objects).zip

b) Layout is changed while open Saved Molfile V2000 file ketcher (Mol 2000).zip

c) Layout is changed while open Saved Molfile V3000 file ketcher (Mol 3000).zip

Expected behavior
Files should open exactly as they were saved.

Versions:
Ketcher version
Version 3.4.0-rc.2 Build at 2025-05-09; 17:40:29
• Indigo Toolkit Version 1.32.0-rc.1.0-g65e26e370-wasm32-wasm-clang-19.0.0
• Chrome Version 136.0.7103.48 (Official Build) (64-bit)
Win11

Issue found while testing #4907