It looks as though Server 10.6.1 has some instabilities regarding SOE management. If I update a SOE directly in Manager, a map service using it will fail to restart, with the dreaded "ClassFactory cannot supply requested class" error. At this point, the only workflow that has worked for me is to delete the SOE from Manager, stop and restart the ArcGIS Server service, add the updated SOE to manager, and re-add it to the map service.
I found this also to be true with a SOE created from scratch using the 10.6.1 template.
Has anyone else seen this problem?