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?
There are a few issues that sound like they may be in play. I'd contact support to see which of these (if any) apply. The second one below sounds like what you're seeing but the criteria described may not match your experience.
[#BUG-000118005: ArcGIS Server logs shows Severe error "ClassFactory cannot supply requested class" during service recycling when multiple pooled services have SOIs enabled]
[BUG-000099727: When server object extensions (SOEs) are deployed to ArcGIS 10.4.1 for Server, and the SOE capability is enabled on more than one service, the process of starting a service configured to use the new capability results in the following error, "0x80040111: ClassFactory cannot supply requested class." This error is generated because the content of the Assembly Cache folder cannot be overwritten at service start.]
[BUG-000112391: A map service with an Server Object Interceptor (SOI) enabled does not process REST requests properly when the map service spawns ArcSOC instances.]
After some more testing, I'm not getting consistent results. It seems to depend on which service hosts the SOE; I was able to attach a sample SOE to SampleWorldCities and update it without any problem, but on another more complex map service, the problem appears. Also, changing maximum instances to 1 makes no difference for that service.