Distorted structure representation when opening saved macromolecules in micro mode in CML, CDX, CDXML, Base 64 CDX formats

**Steps to Reproduce**
1. Open file in Macro mode (Flex mode) [monomers-cycled.zip](https://github.com/user-attachments/files/17281569/monomers-cycled.zip)
2. Switch to Micro mode
3. Save as CML, CDX, CDXML, Base 64 CDX
4. Open saved files

**Actual behavior**
Upon reopening the CML, CDX, CDXML, Base 64 CDX0 files, the structure appears distorted, with bonds incorrectly placed, resulting in a non-cyclic structure (as shown in the screenshot). The original intended shape and arrangement of monomers are lost.
Screen from CDX also not fine:

**Expected behavior**
The saved structure should maintain its original form upon reopening, appearing as a cyclic structure similar to the screenshot.


**Desktop:**
- OS: Windows 11
- Browser Chrome
- Version 128.0.6613.120 (Official Build) (64-bit)

**Ketcher version**
[Version 2.26.0-rc.1]
**Indigo version**
[Version 1.25.0-rc.1]
Bug found during testing: https://github.com/epam/ketcher/issues/5400

Start by reproducing the report with monomers-cycled.zip in Indigo/Ketcher using Micro mode, then save and reopen each listed CML, CDX, CDXML, and Base64 CDX format. Compare the reopened structure with the original cyclic arrangement; done means bonds and monomer geometry remain correct in every format.

Written by the indexing model from the issue text.