See https://knowledge.safe.com/questions/38060/sde-connection-files-and-fme-server.html
I might be OK with read only ArcSDE connection files being in a shared area, but ones with write access need to be restricted. So new system share may be the answer.
If I have a Workspace with a read only ArcSDE connection and a write ArcSDE connection, I can't seem to choose separate locations on server for each one - they both have to go in the same place (that's using FME 2018). So it looks like I will have to create a Workspace with the read only connection file and publish that to upload it to the shared area, then use that in Workspace with the write connection file stored locally.
Is there no way to load ArcSDE connection files into the shared area outside of Workspace publishing? Can you just copy the files to the appropriate folder on the FME Server server?