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Yeah! We had a number of systems at the State of Michigan that, even though we're using BSA for server automation, they had the SCCM client agent left on them with no ill effects.
the main issue is if you do something mutually exclusive via both agents at the same time you will have a bad time. like push a software install via one and reboot in the middle of that via the other.
I think that's pretty much a given!
Kinda like having an admin working remotely on a server while DBAs where onsite trying to install and configure and Oracle database only to have the admin reboot the server right smack in the middle of it! It was a bad day for everyone.
You’d be surprised what people expect to work ☺