Reproduction steps:
1. Open the attached project “BugReport“
2. Open the “Original“ Prefab
3. In the context menu of “My Component“ select “Set My Data B“
4. Save the Prefab

Expected result: Prefab is saved without errors
Actual result: The following error is displayed in the console: Trying to update the managed reference registry with invalid propertyPath(likely caused by a missing reference instance)'managedReferences[7969003593365454855].intValue', with value '6'

Reproduced with: 2021.3.23f1, 2022.2.16f1, 2023.1.0b14, 2023.2.0a13, 2023.3.0.a16
Couldn’t test with: 2020.3.47f1 (The list of [SerializeReference] objects being deserialized is from a more recent version of Unity)

Reproduced on: macOS 13.0.2 (Intel), Windows 10 (user reported)