Once you use the feature, you cannot add or delete a layer comp or layer.
This has always been a known limitation. You will find the same thing
happening with Illustrator files.
Thanks for the clarification!
I guess I was lucky with other files that retained the correct object layer options.
Too bad for this limitation. It makes the whole object layer options feature quiet limited.
I'll add a feature request.
If I have any inkling that I’ll need new layers I add a couple of empty ones to the file before placing it.