Add/Remove hydrogens wipes out custom query features and move some of them to Query specific

**Describe the bug**
Add/Remove hydrogens wipes out custom query features and move some of them to Query specific

**Steps to Reproduce**
1. Load from file: [AddRemove hydrogens wipes out custom query features and move some of them to Query specific.zip](https://github.com/epam/Indigo/files/14433847/AddRemove.hydrogens.wipes.out.custom.query.features.and.move.some.of.them.to.Query.specific.zip)
2. Press Add/Remove explicit hydrogens button

**Actual behavior**
Add/Remove hydrogens wipes out custom query features and move some of them to Query specific

**Expected behavior**
Custom query features remain in place

**Environment details (please complete the following information):**
- Ketcher Version 2.18.0-rc.8 Build at 2024-02-22; 17:34:35
- Indigo Toolkit Version 1.18.0-rc.8.0-g85a393c7c-x86_64-linux-gnu-11.2.1
- Firefox Version 123.0 (64-bit)
- Win10
- Issue found while testing https://github.com/epam/Indigo/issues/1589

Start by reproducing the issue with the attached ZIP and the Add/Remove explicit hydrogens button in the reported Ketcher/Indigo versions. Trace the hydrogens operation and its handling of custom query features; done means those features remain in place after the operation, rather than being wiped out or moved to Query specific.

Written by the indexing model from the issue text.