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Problem: Enabling conditional field dependeny on an entity reference field type using autocomplete will cause that specific field to not be saved or updated. The rest of the node and its fields get saved/updated. Disabling the conditional field module (dependency) on the affected field resolves the issue.
In short, there is something that the conditional fields module is doing that is preventing the saving and updating of an entity reference + autocomplete field type.
The workaround is to just avoid creating a dependency with the conditional field module. If you really need to show/hide a field visually without any fancy validations or checks, then write your own jQuery conditions until this is fixed.
entity type: node
field type: entity reference with autocomplete targeting a node
conditional field dependencies: show a field when a checkbox is a certain value
possible module interferences: entity reference module