Properties that are deprecated are (incorrectly) not currently being propagated to instances by the duplication logic that we use to instance BP-added components as part of Actor-based BP construction logic. The end result is that the archetype (serialized) and the instance (duplicate) do not match after duplication. In turn, this leads the construction logic to infer that the member was modified by the BP's construction script, which is always authoritative over any instance-local edits that the user makes. This is why it no longer shows the serialized (non-default) value, and why it can no longer be toggled.
There's no existing public thread on this issue, so head over to Questions & Answers just mention UE-198568 in the post.