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My initial thoughts would have been to use tagging but i can't think of any way of importing a list into the tags.
If you were running 4.6 i would point you to the WebAPI as it could probably be done that way.
A bit of a long winded way but i think it will work....
1. Create a new empty group in your system tree.
2. Import you list of computers. Choose import system and don't deploy agents. and OK any duplication messages.
3. Run the 'Duplicate System Names' query.
4. Hopefully, if you have no legitimate duplicates, a select all and delete from the query search results will achieve your goal.
Yes, i thought about the tag approach too but did'nt find a way...
Your workaround works perfect using the import and ticking the option to move the existing machines from other containers to this one.
Create a server task to "Load Systems by File" with a sub action of deleting them. Or, the sub action can be to tag them. Then you can look at them and delete them manually from the system tree.