There is no way to unregister a SDE layer in an enterprise SDE database. The only option catalog gives me is to delete it which is a very destructive operation. This means all the triggers, data, indexes and EVERYTHING to do with that table is lost.
I propose, the ability to de-register a table from Catalog without deleting the table.
Post on the issue with discussion found at - https://community.esri.com/message/902166-re-why-cant-a-layer-be-de-registered-with-the-sde?commentID=902166&et=watches.email.thread#comment-902166