Layers not emitted when used as colors of probes with separate elaboration

[dtzSiFive]

Type of issue: Bug Report

Please provide the steps to reproduce the problem:

1. Checkout this commit of Chisel (small change to test to demonstrate issue):

4932549

2. testOnly chiselTests.experimental.hierarchy.SeparateElaborationSpec (I did this by launching sbt and entering this at the prompt)

What is the current behavior?

Errors due to generated FIRRTL using layers that aren't declared:

[info] src/test/scala/chiselTests/experimental/hierarchy/Examples.scala:43:23: error: probe port 'p' is associated with layer '@A', but this layer was not defined
[info]     @public val p = IO(probe.Probe(UInt(width.W), A))

What is the expected behavior?

All used layers are emitted, no error when using layer-colored probes in this way.

Please tell us about your environment:

Other Information

What is the use case for changing the behavior?