I've created a new 'site' and performed a new AD Import to that site, then sent an Agent Wakeup call to the site. I'm going to go back in a bit and see what statuses have updated.
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I've moved your post to the ePO forum for better attention.
Not that i can help much with the AD sync issues- 3.6.1 was notorious for duplicate machine names.
Another point is - do you want to upgrade twice- go to 8.5 then 8.7?
Why not just setup your new server (fresh install), deploy your agent and do one upgrade. It seems like more hassle and I'm sure you've been through enough by the sounds of things!
the quicker you can move to 4.5 the better- and believe me- 4.5 is HEAPS better than 3.6 or 3.6.1. (or NA mgmt console 2.5 for that matter! )
I'm just finfishing my migration from 3.6.1 to 4.5
I pushed ahead and jumped to 4.5, and almost all issues have been solved
We still have a couple of machines refusing updates, but that's down to their individual (highly restrictive) security settings, I believe.
Glad to hear it